Substituted nucleotide analogs

ABSTRACT

Disclosed herein are phosphorothioate nucleotide analogs, methods of synthesizing phosphorothioate nucleotide analogs and methods of treating diseases and/or conditions such as viral infections, cancer, and/or parasitic diseases with the phosphorothioate nucleotide analogs.

This application is a continuation of U.S. application Ser. No. 13/722,472, filed Dec. 20, 2012 which claims the benefit of U.S. Provisional Application No. 61/579,533, filed Dec. 22, 2011; which are both incorporated herein by reference in their entireties; including any drawings.

BACKGROUND

1. Field

The present application relates to the fields of chemistry, biochemistry and medicine. More particularly, disclosed herein are phosphorothioate nucleotide analogs, pharmaceutical compositions that include one or more phosphorothioate nucleotide analogs and methods of synthesizing the same. Also disclosed herein are methods of treating diseases and/or conditions with a phosphorothioate nucleotide analog, alone or in combination therapy with other agents.

2. Description

Nucleoside analogs are a class of compounds that have been shown to exert antiviral and anticancer activity both in vitro and in vivo, and thus, have been the subject of widespread research for the treatment of viral infections and cancer. Nucleoside analogs are usually therapeutically inactive compounds that are converted by host or viral enzymes to their respective active anti-metabolites, which, in turn, may inhibit polymerases involved in viral or cell proliferation. The activation occurs by a variety of mechanisms, such as the addition of one or more phosphate groups and, or in combination with, other metabolic processes.

SUMMARY

Some embodiments disclosed herein relate to a compound of Formula (I) or a pharmaceutically acceptable salt thereof

Some embodiments disclosed herein relate to a method of ameliorating and/or treating a neoplastic disease that can include administering to a subject suffering from the neoplastic disease a therapeutically effective amount of one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for ameliorating and/or treating a neoplastic disease. Still other embodiments described herein relate to one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, that can be used for ameliorating and/or treating a neoplastic disease.

Some embodiments disclosed herein relate to a method of inhibiting the growth of a tumor that can include administering to a subject having a tumor a therapeutically effective amount of one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for inhibiting the growth of a tumor. Still other embodiments described herein relate to one or more compounds of Formula (I), or a pharmaceutically acceptable salt of thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, that can be used for inhibiting the growth of a tumor.

Some embodiments disclosed herein relate to a method of ameliorating and/or treating a viral infection that can include administering to a subject identified as suffering from the viral infection a therapeutically effective amount of one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for ameliorating and/or treating a viral infection. Still other embodiments described herein relate to one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, that can be used for ameliorating and/or treating a viral infection.

Some embodiments disclosed herein relate to a method of ameliorating and/or treating a viral infection that can include contacting a cell infected with the virus with an effective amount of one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, in the manufacture of a medicament for ameliorating and/or treating a viral infection that can include contacting a cell infected with the virus with an effective amount of said compound(s). Still other embodiments described herein relate to one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof, that can be used for ameliorating and/or treating a viral infection by contacting a cell infected with the virus with an effective amount of said compound(s).

Some embodiments disclosed herein relate to a method of inhibiting replication of a virus that can include contacting a cell infected with the virus with an effective amount of one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, in the manufacture of a medicament for inhibiting replication of a virus that can include contacting a cell infected with the virus with an effective amount of said compound(s). Still other embodiments described herein relate to one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof, that can be used for inhibiting replication of a virus by contacting a cell infected with the virus with an effective amount of said compound(s).

Some embodiments disclosed herein relate to a method of ameliorating and/or treating a parasitic disease that can include administering to a subject suffering from the parasitic disease a therapeutically effective amount of one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for ameliorating and/or treating a parasitic disease. Still other embodiments described herein relate to one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, that can be used for ameliorating and/or treating a parasitic disease.

Some embodiments disclosed herein relate to a method of ameliorating and/or treating a viral infection that can include administering to a subject identified as suffering from the viral infection a therapeutically effective amount of a compound described herein or a pharmaceutically acceptable salt thereof (for example, one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof), or a pharmaceutical composition that includes a compound described herein, or a pharmaceutically acceptable salt thereof, in combination with an agent selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an other antiviral compound, a compound of Formula (BB) and a compound of Formula (CC), or a pharmaceutically acceptable salt of any of the foregoing. Some embodiments disclosed herein relate to a method of ameliorating and/or treating a viral infection that can include contacting a cell infected with the viral infection with a therapeutically effective amount of a compound described herein or a pharmaceutically acceptable salt thereof (for example, one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof), or a pharmaceutical composition that includes a compound described herein, in combination with an agent selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an other antiviral compound, a compound of Formula (BB) and a compound of Formula (CC), or a pharmaceutically acceptable salt of any of the foregoing. Some embodiments disclosed herein relate to a method of inhibiting replication of a virus that can include administering to a subject identified as being infected with the virus a therapeutically effective amount of a compound described herein or a pharmaceutically acceptable salt thereof (for example, a compound of Formula (I), or a pharmaceutically acceptable salt thereof), or a pharmaceutical composition that includes a compound described herein, or a pharmaceutically acceptable salt thereof, in combination with an agent selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an other antiviral compound, or a pharmaceutically acceptable salt of any of the foregoing. In some embodiments, the agent can be a compound, or a pharmaceutically acceptable salt thereof, selected from Compound 1001-1016, 2001-2012, 3001-3014, 4001-4012, 5001-5011, 6001-6078 and 7000-7016, or a pharmaceutical composition that includes one or more of the aforementioned compounds, or pharmaceutically acceptable salt thereof. In some embodiments, the method can include administering a second agent selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an other antiviral compound, a compound of Formula (BB) and a compound of Formula (CC), or a pharmaceutically acceptable salt of any of the foregoing. In some embodiments, the viral infection can be HCV.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows example HCV protease inhibitors.

FIG. 2 shows example nucleoside HCV polymerase inhibitors.

FIG. 3 shows example non-nucleoside HCV polymerase inhibitors.

FIG. 4 shows example NS5A inhibitors.

FIG. 5 shows example other antivirals.

FIG. 6 shows example compounds of Formula (CC), and alpha-thiotriphosphates thereof

FIG. 7 shows example compounds of Formula (BB).

FIG. 8 shows example compounds of Formula (I).

DETAILED DESCRIPTION

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art. All patents, applications, published applications and other publications referenced herein are incorporated by reference in their entirety unless stated otherwise. In the event that there are a plurality of definitions for a term herein, those in this section prevail unless stated otherwise.

As used herein, any “R” group(s) such as, without limitation, R, R¹, R², R³, R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, R¹⁴, R¹⁵, R^(3A), R^(4A) and R^(5A) represent substituents that can be attached to the indicated atom. An R group may be substituted or unsubstituted. If two “R” groups are described as being “taken together” the R groups and the atoms they are attached to can form a cycloalkyl, cycloalkenyl, aryl, heteroaryl or heterocycle. For example, without limitation, if R^(a) and R^(b) of an NR^(a)R^(b) group are indicated to be “taken together,” it means that they are covalently bonded to one another to form a ring:

In addition, if two “R” groups are described as being “taken together” with the atom(s) to which they are attached to form a ring as an alternative, the R groups are not limited to the variables or substituents defined previously.

Whenever a group is described as being “optionally substituted” that group may be unsubstituted or substituted with one or more of the indicated substituents. Likewise, when a group is described as being “unsubstituted or substituted” if substituted, the substituent(s) may be selected from one or more of the indicated substituents. If no substituents are indicated, it is meant that the indicated “optionally substituted” or “substituted” group may be substituted with one or more group(s) individually and independently selected from alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, hydroxy, protected hydroxyl, alkoxy, aryloxy, acyl, mercapto, alkylthio, arylthio, cyano, halogen, thiocarbonyl, O-carbamyl, N-carbamyl, O-thiocarbamyl, N-thiocarbamyl, C-amido, N-amido, S-sulfonamido, N-sulfonamido, C-carboxy, protected C-carboxy, O-carboxy, isocyanato, thiocyanato, isothiocyanato, nitro, silyl, sulfenyl, sulfinyl, sulfonyl, haloalkyl, haloalkoxy, trihalomethanesulfonyl, trihalomethanesulfonamido, an amino, a mono-substituted amino group and a di-substituted amino group, and protected derivatives thereof

As used herein, “C_(a) to C_(b)” in which “a” and “b” are integers refer to the number of carbon atoms in an alkyl, alkenyl or alkynyl group, or the number of carbon atoms in the ring of a cycloalkyl, cycloalkenyl, aryl, heteroaryl or heteroalicyclyl group. That is, the alkyl, alkenyl, alkynyl, ring of the cycloalkyl, ring of the cycloalkenyl, ring of the aryl, ring of the heteroaryl or ring of the heteroalicyclyl can contain from “a” to “b”, inclusive, carbon atoms. Thus, for example, a “C₁ to C₄ alkyl” group refers to all alkyl groups having from 1 to 4 carbons, that is, CH₃—, CH₃CH₂—, CH₃CH₂CH₂—, (CH₃)₂CH—, CH₃CH₂CH₂CH₂—, CH₃CH₂CH(CH₃)— and (CH₃)₃C—. If no “a” and “b” are designated with regard to an alkyl, alkenyl, alkynyl, cycloalkyl cycloalkenyl, aryl, heteroaryl or heteroalicyclyl group, the broadest range described in these definitions is to be assumed.

As used herein, “alkyl” refers to a straight or branched hydrocarbon chain that comprises a fully saturated (no double or triple bonds) hydrocarbon group. The alkyl group may have 1 to 20 carbon atoms (whenever it appears herein, a numerical range such as “1 to 20” refers to each integer in the given range; e.g., “1 to 20 carbon atoms” means that the alkyl group may consist of 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc., up to and including 20 carbon atoms, although the present definition also covers the occurrence of the term “alkyl” where no numerical range is designated). The alkyl group may also be a medium size alkyl having 1 to 10 carbon atoms. The alkyl group could also be a lower alkyl having 1 to 6 carbon atoms. The alkyl group of the compounds may be designated as “C₁-C₄ alkyl” or similar designations. By way of example only, “C₁-C₄ alkyl” indicates that there are one to four carbon atoms in the alkyl chain, i.e., the alkyl chain is selected from methyl, ethyl, propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl, and t-butyl. Typical alkyl groups include, but are in no way limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tertiary butyl, pentyl and hexyl. The alkyl group may be substituted or unsubstituted.

As used herein, “alkenyl” refers to an alkyl group that contains in the straight or branched hydrocarbon chain one or more double bonds. An alkenyl group may be unsubstituted or substituted.

As used herein, “alkynyl” refers to an alkyl group that contains in the straight or branched hydrocarbon chain one or more triple bonds. An alkynyl group may be unsubstituted or substituted.

As used herein, “cycloalkyl” refers to a completely saturated (no double or triple bonds) mono- or multi-cyclic hydrocarbon ring system. When composed of two or more rings, the rings may be joined together in a fused fashion. Cycloalkyl groups can contain 3 to 10 atoms in the ring(s) or 3 to 8 atoms in the ring(s). A cycloalkyl group may be unsubstituted or substituted. Typical cycloalkyl groups include, but are in no way limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl and cyclooctyl.

As used herein, “cycloalkenyl” refers to a mono- or multi-cyclic hydrocarbon ring system that contains one or more double bonds in at least one ring; although, if there is more than one, the double bonds cannot form a fully delocalized pi-electron system throughout all the rings (otherwise the group would be “aryl,” as defined herein). When composed of two or more rings, the rings may be connected together in a fused fashion. A cycloalkenyl group may be unsubstituted or substituted.

As used herein, “aryl” refers to a carbocyclic (all carbon) monocyclic or multicyclic aromatic ring system (including fused ring systems where two carbocyclic rings share a chemical bond) that has a fully delocalized pi-electron system throughout all the rings. The number of carbon atoms in an aryl group can vary. For example, the aryl group can be a C₆-C₁₄ aryl group, a C₆-C₁₀ aryl group, or a C₆ aryl group. Examples of aryl groups include, but are not limited to, benzene, naphthalene and azulene. An aryl group may be substituted or unsubstituted.

As used herein, “heteroaryl” refers to a monocyclic or multicyclic aromatic ring system (a ring system with fully delocalized pi-electron system) that contain(s) one or more heteroatoms, that is, an element other than carbon, including but not limited to, nitrogen, oxygen and sulfur. The number of atoms in the ring(s) of a heteroaryl group can vary. For example, the heteroaryl group can contain 4 to 14 atoms in the ring(s), 5 to 10 atoms in the ring(s) or 5 to 6 atoms in the ring(s). Furthermore, the term “heteroaryl” includes fused ring systems where two rings, such as at least one aryl ring and at least one heteroaryl ring, or at least two heteroaryl rings, share at least one chemical bond. Examples of heteroaryl rings include, but are not limited to, furan, furazan, thiophene, benzothiophene, phthalazine, pyrrole, oxazole, benzoxazole, 1,2,3-oxadiazole, 1,2,4-oxadiazole, thiazole, 1,2,3-thiadiazole, 1,2,4-thiadiazole, benzothiazole, imidazole, benzimidazole, indole, indazole, pyrazole, benzopyrazole, isoxazole, benzoisoxazole, isothiazole, triazole, benzotriazole, thiadiazole, tetrazole, pyridine, pyridazine, pyrimidine, pyrazine, purine, pteridine, quinoline, isoquinoline, quinazoline, quinoxaline, cinnoline, and triazine. A heteroaryl group may be substituted or unsubstituted.

As used herein, “heterocyclyl” or “heteroalicyclyl” refers to three-, four-, five-, six-, seven-, eight-, nine-, ten-, up to 18-membered monocyclic, bicyclic, and tricyclic ring system wherein carbon atoms together with from 1 to 5 heteroatoms constitute said ring system. A heterocycle may optionally contain one or more unsaturated bonds situated in such a way, however, that a fully delocalized pi-electron system does not occur throughout all the rings. The heteroatom(s) is an element other than carbon including, but not limited to, oxygen, sulfur, and nitrogen. A heterocycle may further contain one or more carbonyl or thiocarbonyl functionalities, so as to make the definition include oxo-systems and thio-systems such as lactams, lactones, cyclic imides, cyclic thioimides and cyclic carbamates. When composed of two or more rings, the rings may be joined together in a fused fashion. Additionally, any nitrogens in a heteroalicyclic may be quaternized. Heterocyclyl or heteroalicyclic groups may be unsubstituted or substituted. Examples of such “heterocyclyl” or “heteroalicyclyl” groups include but are not limited to, 1,3-dioxin, 1,3-dioxane, 1,4-dioxane, 1,2-dioxolane, 1,3-dioxolane, 1,4-dioxolane, 1,3-oxathiane, 1,4-oxathiin, 1,3-oxathiolane, 1,3-dithiole, 1,3-dithiolane, 1,4-oxathiane, tetrahydro-1,4-thiazine, 2H-1,2-oxazine, maleimide, succinimide, barbituric acid, thiobarbituric acid, dioxopiperazine, hydantoin, dihydrouracil, trioxane, hexahydro-1,3,5-triazine, imidazoline, imidazolidine, isoxazoline, isoxazolidine, oxazoline, oxazolidine, oxazolidinone, thiazoline, thiazolidine, morpholine, oxirane, piperidine N-Oxide, piperidine, piperazine, pyrrolidine, pyrrolidone, pyrrolidione, 4-piperidone, pyrazoline, pyrazolidine, 2-oxopyrrolidine, tetrahydropyran, 4H-pyran, tetrahydrothiopyran, thiamorpholine, thiamorpholine sulfoxide, thiamorpholine sulfone, and their benzo-fused analogs (e.g., benzimidazolidinone, tetrahydroquinoline and 3,4-methylenedioxyphenyl).

As used herein, “aralkyl” and “aryl(alkyl)” refer to an aryl group connected, as a substituent, via a lower alkylene group. The lower alkylene and aryl group of an aralkyl may be substituted or unsubstituted. Examples include but are not limited to benzyl, 2-phenylalkyl, 3-phenylalkyl, and naphthylalkyl.

As used herein, “heteroaralkyl” and “heteroaryl(alkyl)” refer to a heteroaryl group connected, as a substituent, via a lower alkylene group. The lower alkylene and heteroaryl group of heteroaralkyl may be substituted or unsubstituted. Examples include but are not limited to 2-thienylalkyl, 3-thienylalkyl, furylalkyl, thienylalkyl, pyrrolylalkyl, pyridylalkyl, isoxazolylalkyl, imidazolylalkyl and their benzo-fused analogs.

A “(heteroalicyclyl)alkyl” and “(heterocyclyl)alkyl” refer to a heterocyclic or a heteroalicyclylic group connected, as a substituent, via a lower alkylene group. The lower alkylene and heterocyclyl of a (heteroalicyclyl)alkyl may be substituted or unsubstituted. Examples include but are not limited tetrahydro-2H-pyran-4-yl)methyl, (piperidin-4-yl)ethyl, (piperidin-4-yl)propyl, (tetrahydro-2H-thiopyran-4-yl)methyl, and (1,3-thiazinan-4-yl)methyl.

“Lower alkylene groups” are straight-chained —CH₂— tethering groups, forming bonds to connect molecular fragments via their terminal carbon atoms. Examples include but are not limited to methylene (—CH₂—), ethylene (—CH₂CH₂—), propylene (—CH₂CH₂CH₂—), and butylene (—CH₂CH₂CH₂CH₂—). A lower alkylene group can be substituted by replacing one or more hydrogen of the lower alkylene group with a substituent(s) listed under the definition of “substituted.”

As used herein, “alkoxy” refers to the formula —OR wherein R is an alkyl, an alkenyl, an alkynyl, a cycloalkyl, a cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl is defined herein. A non-limiting list of alkoxys are methoxy, ethoxy, n-propoxy, 1-methylethoxy(isopropoxy), n-butoxy, iso-butoxy, sec-butoxy, tert-butoxy, phenoxy and benzoxy. An alkoxy may be substituted or unsubstituted.

As used herein, “acyl” refers to a hydrogen, alkyl, alkenyl, alkynyl, or aryl connected, as substituents, via a carbonyl group. Examples include formyl, acetyl, propanoyl, benzoyl, and acryl. An acyl may be substituted or unsubstituted.

As used herein, “hydroxyalkyl” refers to an alkyl group in which one or more of the hydrogen atoms are replaced by a hydroxy group. Exemplary hydroxyalkyl groups include but are not limited to, 2-hydroxyethyl, 3-hydroxypropyl, 2-hydroxypropyl, and 2,2-dihydroxyethyl. A hydroxyalkyl may be substituted or unsubstituted.

As used herein, “haloalkyl” refers to an alkyl group in which one or more of the hydrogen atoms are replaced by a halogen (e.g., mono-haloalkyl, di-haloalkyl and tri-haloalkyl). Such groups include but are not limited to, chloromethyl, fluoromethyl, difluoromethyl, trifluoromethyl, 1-chloro-2-fluoromethyl and 2-fluoroisobutyl. A haloalkyl may be substituted or unsubstituted.

As used herein, “haloalkoxy” refers to an alkoxy group in which one or more of the hydrogen atoms are replaced by a halogen (e.g., mono-haloalkoxy, di-haloalkoxy and tri-haloalkoxy). Such groups include but are not limited to, chloromethoxy, fluoromethoxy, difluoromethoxy, trifluoromethoxy, 1-chloro-2-fluoromethoxy and 2-fluoroisobutoxy. A haloalkoxy may be substituted or unsubstituted.

As used herein, “arylthio” refers to RS—, in which R is an aryl, such as, but not limited to, phenyl. An arylthio may be substituted or unsubstituted.

A “sulfenyl” group refers to an “—SR” group in which R can be hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl. A sulfenyl may be substituted or unsubstituted.

A “sulfinyl” group refers to an “—S(═O)—R” group in which R can be the same as defined with respect to sulfenyl. A sulfinyl may be substituted or unsubstituted.

A “sulfonyl” group refers to an “SO₂R” group in which R can be the same as defined with respect to sulfenyl. A sulfonyl may be substituted or unsubstituted.

An “O-carboxy” group refers to a “RC(═O)O-” group in which R can be hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl, as defined herein. An O-carboxy may be substituted or unsubstituted.

The terms “ester” and “C-carboxy” refer to a “—C(═O)OR” group in which R can be the same as defined with respect to O-carboxy. An ester and C-carboxy may be substituted or unsubstituted.

A “thiocarbonyl” group refers to a “—C(═S)R” group in which R can be the same as defined with respect to O-carboxy. A thiocarbonyl may be substituted or unsubstituted.

A “trihalomethanesulfonyl” group refers to an “X₃CSO₂-” group wherein each X is a halogen.

A “trihalomethanesulfonamido” group refers to an “X₃CS(O)₂N(R_(A))—” group wherein each X is a halogen, and R_(A) hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl.

The term “amino” as used herein refers to a —NH₂ group.

As used herein, the term “hydroxy” refers to a —OH group.

A “cyano” group refers to a “—CN” group.

The term “azido” as used herein refers to a —N₃ group.

An “isocyanato” group refers to a “—NCO” group.

A “thiocyanato” group refers to a “—CNS” group.

An “isothiocyanato” group refers to an “—NCS” group.

A “mercapto” group refers to an “—SH” group.

A “carbonyl” group refers to a C═O group.

An “S-sulfonamido” group refers to a “—SO₂N(R_(A)R_(B))” group in which R_(A) and R_(B) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl. An S-sulfonamido may be substituted or unsubstituted.

An “N-sulfonamido” group refers to a “RSO₂N(R_(A))—” group in which R and R_(A) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl. An N-sulfonamido may be substituted or unsubstituted.

An “O-carbamyl” group refers to a “—OC(═O)N(R_(A)R_(B))” group in which R_(A) and R_(B) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl. An 0-carbamyl may be substituted or unsubstituted.

An “N-carbamyl” group refers to an “ROC(═O)N(R_(A))—” group in which R and R_(A) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl. An N-carbamyl may be substituted or unsubstituted.

An “O-thiocarbamyl” group refers to a “—OC(═S)—N(R_(A)R_(B))” group in which R_(A) and R_(B) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl. An O-thiocarbamyl may be substituted or unsubstituted.

An “N-thiocarbamyl” group refers to an “ROC(═S)N(R_(A))—” group in which R and R_(A) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl. An N-thiocarbamyl may be substituted or unsubstituted.

A “C-amido” group refers to a “—C(═O)N(R_(A)R_(B))” group in which R_(A) and R_(B) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl. A C-amido may be substituted or unsubstituted.

An “N-amido” group refers to a “RC(═O)N(R_(A))—” group in which R and R_(A) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, (heteroaryl)alkyl or (heteroalicyclyl)alkyl. An N-amido may be substituted or unsubstituted.

The term “halogen atom” or “halogen” as used herein, means any one of the radio-stable atoms of column 7 of the Periodic Table of the Elements, such as, fluorine, chlorine, bromine and iodine.

Where the numbers of substituents is not specified (e.g. haloalkyl), there may be one or more substituents present. For example “haloalkyl” may include one or more of the same or different halogens. As another example, “C₁-C₃ alkoxyphenyl” may include one or more of the same or different alkoxy groups containing one, two or three atoms.

As used herein, the abbreviations for any protective groups, amino acids and other compounds, are, unless indicated otherwise, in accord with their common usage, recognized abbreviations, or the IUPAC-IUB Commission on Biochemical Nomenclature (See, Biochem. 11:942-944 (1972)).

The term “nucleoside” is used herein in its ordinary sense as understood by those skilled in the art, and refers to a compound composed of an optionally substituted pentose moiety or modified pentose moiety attached to a heterocyclic base or tautomer thereof via a N-glycosidic bond, such as attached via the 9-position of a purine-base or the 1-position of a pyrimidine-base. Examples include, but are not limited to, a ribonucleoside comprising a ribose moiety and a deoxyribonucleoside comprising a deoxyribose moiety. A modified pentose moiety is a pentose moiety in which an oxygen atom has been replaced with a carbon and/or a carbon has been replaced with a sulfur or an oxygen atom. A “nucleoside” is a monomer that can have a substituted base and/or sugar moiety. Additionally, a nucleoside can be incorporated into larger DNA and/or RNA polymers and oligomers. In some instances, the nucleoside can be a nucleoside analog drug.

As used herein, the term “heterocyclic base” refers to an optionally substituted nitrogen-containing heterocyclyl that can be attached to an optionally substituted pentose moiety or modified pentose moiety. In some embodiments, the heterocyclic base can be selected from an optionally substituted purine-base, an optionally substituted pyrimidine-base and an optionally substituted triazole-base (for example, a 1,2,4-triazole). The term “purine-base” is used herein in its ordinary sense as understood by those skilled in the art, and includes its tautomers. Similarly, the term “pyrimidine-base” is used herein in its ordinary sense as understood by those skilled in the art, and includes its tautomers. A non-limiting list of optionally substituted purine-bases includes purine, adenine, guanine, hypoxanthine, xanthine, alloxanthine, 7-alkylguanine (e.g. 7-methylguanine), theobromine, caffeine, uric acid and isoguanine. Examples of pyrimidine-bases include, but are not limited to, cytosine, thymine, uracil, 5,6-dihydrouracil and 5-alkylcytosine (e.g., 5-methylcytosine). An example of an optionally substituted triazole-base is 1,2,4-triazole-3-carboxamide. Other non-limiting examples of heterocyclic bases include diaminopurine, 8-oxo-N⁶-alkyladenine (e.g., 8-oxo-N⁶-methyladenine), 7-deazaxanthine, 7-deazaguanine, 7-deazaadenine, N⁴,N⁴-ethanocytosin, N⁶,N⁶-ethano-2,6-diaminopurine, 5-halouracil (e.g., 5-fluorouracil and 5-bromouracil), pseudoisocytosine, isocytosine, isoguanine, and other heterocyclic bases described in U.S. Pat. Nos. 5,432,272 and 7,125,855, which are incorporated herein by reference for the limited purpose of disclosing additional heterocyclic bases. In some embodiments, a heterocyclic base can be optionally substituted with an amine or an enol protecting group(s).

The term “—N-linked amino acid” refers to an amino acid that is attached to the indicated moiety via a main-chain amino or mono-substituted amino group. When the amino acid is attached in an —N-linked amino acid, one of the hydrogens that is part of the main-chain amino or mono-substituted amino group is not present and the amino acid is attached via the nitrogen. As used herein, the term “amino acid” refers to any amino acid (both standard and non-standard amino acids), including, but not limited to, α-amino acids, β-amino acids, γ-amino acids and δ-amino acids. Examples of suitable amino acids include, but are not limited to, alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, tyrosine, arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Additional examples of suitable amino acids include, but are not limited to, ornithine, hypusine, 2-aminoisobutyric acid, dehydroalanine, gamma-aminobutyric acid, citrulline, beta-alanine, alpha-ethyl-glycine, alpha-propyl-glycine and norleucine. N-linked amino acids can be substituted or unsubstituted.

The term “—N-linked amino acid ester derivative” refers to an amino acid in which a main-chain carboxylic acid group has been converted to an ester group. In some embodiments, the ester group has a formula selected from alkyl-O—C(═O)—, cycloalkyl-O—C(═O)—, aryl-O—C(═O)— and aryl(alkyl)-O—C(═O)—. A non-limiting list of ester groups include substituted and unsubstituted versions of the following: methyl-O—C(═O)—, ethyl-O—C(═O)—, n-propyl-O—C(═O)—, isopropyl-O—C(═O)—, n-butyl-O—C(═O)—, isobutyl-O—C(═O)—, tert-butyl-O—C(═O)—, neopentyl-O—C(═O)—, cyclopropyl-O—C(═O)—, cyclobutyl-O—C(═O)—, cyclopentyl-O—C(═O)—, cyclohexyl-O—C(═O)—, phenyl-O—C(═O)—, benzyl-O—C(═O)—)—, and naphthyl-O—C(═O)—. N-linked amino acid ester derivatives can be substituted or unsubstituted.

The terms “protecting group” and “protecting groups” as used herein refer to any atom or group of atoms that is added to a molecule in order to prevent existing groups in the molecule from undergoing unwanted chemical reactions. Examples of protecting group moieties are described in T. W. Greene and P. G. M. Wuts, Protective Groups in Organic Synthesis, 3. Ed. John Wiley & Sons, 1999, and in J. F. W. McOmie, Protective Groups in Organic Chemistry Plenum Press, 1973, both of which are hereby incorporated by reference for the limited purpose of disclosing suitable protecting groups. The protecting group moiety may be chosen in such a way, that they are stable to certain reaction conditions and readily removed at a convenient stage using methodology known from the art. A non-limiting list of protecting groups include benzyl; substituted benzyl; alkylcarbonyls and alkoxycarbonyls (e.g., t-butoxycarbonyl (BOC), acetyl, or isobutyryl); arylalkylcarbonyls and arylalkoxycarbonyls (e.g., benzyloxycarbonyl); substituted methyl ether (e.g. methoxymethyl ether); substituted ethyl ether; a substituted benzyl ether; tetrahydropyranyl ether; silyls (e.g., trimethylsilyl, triethylsilyl, triisopropylsilyl, t-butyldimethylsilyl, tri-iso-propylsilyloxymethyl, [2-(trimethylsilyl)ethoxy]methyl or t-butyldiphenylsilyl); esters (e.g. benzoate ester); carbonates (e.g. methoxymethylcarbonate); sulfonates (e.g. tosylate or mesylate); acyclic ketal (e.g. dimethyl acetal); cyclic ketals (e.g., 1,3-dioxane, 1,3-dioxolanes, and those described herein); acyclic acetal; cyclic acetal (e.g., those described herein); acyclic hemiacetal; cyclic hemiacetal; cyclic dithioketals (e.g., 1,3-dithiane or 1,3-dithiolane); orthoesters (e.g., those described herein) and triarylmethyl groups (e.g., trityl; monomethoxytrityl (MMTr); 4,4′-dimethoxytrityl (DMTr); 4,4′,4″-trimethoxytrityl (TMTr); and those described herein).

“Leaving group” as used herein refers to any atom or moiety that is capable of being displaced by another atom or moiety in a chemical reaction. More specifically, in some embodiments, “leaving group” refers to the atom or moiety that is displaced in a nucleophilic substitution reaction. In some embodiments, “leaving groups” are any atoms or moieties that are conjugate bases of strong acids. Examples of suitable leaving groups include, but are not limited to, tosylates and halogens. Non-limiting characteristics and examples of leaving groups can be found, for example in Organic Chemistry, 2d ed., Francis Carey (1992), pages 328-331; Introduction to Organic Chemistry, 2d ed., Andrew Streitwieser and Clayton Heathcock (1981), pages 169-171; and Organic Chemistry, 5^(th) ed., John McMurry (2000), pages 398 and 408; all of which are incorporated herein by reference for the limited purpose of disclosing characteristics and examples of leaving groups.

The term “pharmaceutically acceptable salt” refers to a salt of a compound that does not cause significant irritation to an organism to which it is administered and does not abrogate the biological activity and properties of the compound. In some embodiments, the salt is an acid addition salt of the compound. Pharmaceutical salts can be obtained by reacting a compound with inorganic acids such as hydrohalic acid (e.g., hydrochloric acid or hydrobromic acid), sulfuric acid, nitric acid and phosphoric acid. Pharmaceutical salts can also be obtained by reacting a compound with an organic acid such as aliphatic or aromatic carboxylic or sulfonic acids, for example formic, acetic, succinic, lactic, malic, tartaric, citric, ascorbic, nicotinic, methanesulfonic, ethanesulfonic, p-toluensulfonic, salicylic or naphthalenesulfonic acid. Pharmaceutical salts can also be obtained by reacting a compound with a base to form a salt such as an ammonium salt, an alkali metal salt, such as a sodium or a potassium salt, an alkaline earth metal salt, such as a calcium or a magnesium salt, a salt of organic bases such as dicyclohexylamine, N-methyl-D-glucamine, tris(hydroxymethyl)methylamine, C₁-C₇ alkylamine, cyclohexylamine, triethanolamine, ethylenediamine, and salts with amino acids such as arginine and lysine.

Terms and phrases used in this application, and variations thereof, especially in the appended claims, unless otherwise expressly stated, should be construed as open ended as opposed to limiting. As examples of the foregoing, the term ‘including’ should be read to mean ‘including, without limitation,’ ‘including but not limited to,’ or the like; the term ‘comprising’ as used herein is synonymous with ‘including,’ ‘containing,’ or ‘characterized by,’ and is inclusive or open-ended and does not exclude additional, unrecited elements or method steps; the term ‘having’ should be interpreted as ‘having at least;’ the term ‘includes’ should be interpreted as ‘includes but is not limited to;’ the term ‘example’ is used to provide exemplary instances of the item in discussion, not an exhaustive or limiting list thereof; and use of terms like ‘preferably,’ ‘preferred,’ ‘desired,’ or ‘desirable,’ and words of similar meaning should not be understood as implying that certain features are critical, essential, or even important to the structure or function of the invention, but instead as merely intended to highlight alternative or additional features that may or may not be utilized in a particular embodiment. In addition, the term “comprising” is to be interpreted synonymously with the phrases “having at least” or “including at least”. When used in the context of a process, the term “comprising” means that the process includes at least the recited steps, but may include additional steps. When used in the context of a compound, composition or device, the term “comprising” means that the compound, composition or device includes at least the recited features or components, but may also include additional features or components. Likewise, a group of items linked with the conjunction ‘and’ should not be read as requiring that each and every one of those items be present in the grouping, but rather should be read as ‘and/or’ unless expressly stated otherwise. Similarly, a group of items linked with the conjunction ‘or’ should not be read as requiring mutual exclusivity among that group, but rather should be read as ‘and/or’ unless expressly stated otherwise.

With respect to the use of substantially any plural and/or singular terms herein, those having skill in the art can translate from the plural to the singular and/or from the singular to the plural as is appropriate to the context and/or application. The various singular/plural permutations may be expressly set forth herein for sake of clarity. The indefinite article “a” or “an” does not exclude a plurality. A single processor or other unit may fulfill the functions of several items recited in the claims. The mere fact that certain measures are recited in mutually different dependent claims does not indicate that a combination of these measures cannot be used to advantage. Any reference signs in the claims should not be construed as limiting the scope.

It is understood that, in any compound described herein having one or more chiral centers, if an absolute stereochemistry is not expressly indicated, then each center may independently be of R-configuration or S-configuration or a mixture thereof. Thus, the compounds provided herein may be enantiomerically pure, enantiomerically enriched, racemic mixture, diastereomerically pure, diastereomerically enriched, or a stereoisomeric mixture. In addition it is understood that, in any compound described herein having one or more double bond(s) generating geometrical isomers that can be defined as E or Z, each double bond may independently be E or Z a mixture thereof

Likewise, it is understood that, in any compound described, all tautomeric forms are also intended to be included. For example all tautomers of a phosphate and a phosphorothioate groups are intended to be included. Examples of tautomers of a phosphorothioate include the following:

Furthermore, all tautomers of heterocyclic bases known in the art are intended to be included, including tautomers of natural and non-natural purine-bases and pyrimidine-bases.

It is to be understood that where compounds disclosed herein have unfilled valencies, then the valencies are to be filled with hydrogens or isotopes thereof, e.g., hydrogen-1 (protium) and hydrogen-2 (deuterium).

It is understood that the compounds described herein can be labeled isotopically. Substitution with isotopes such as deuterium may afford certain therapeutic advantages resulting from greater metabolic stability, such as, for example, increased in vivo half-life or reduced dosage requirements. Each chemical element as represented in a compound structure may include any isotope of said element. For example, in a compound structure a hydrogen atom may be explicitly disclosed or understood to be present in the compound. At any position of the compound that a hydrogen atom may be present, the hydrogen atom can be any isotope of hydrogen, including but not limited to hydrogen-1 (protium) and hydrogen-2 (deuterium). Thus, reference herein to a compound encompasses all potential isotopic forms unless the context clearly dictates otherwise.

It is understood that the methods and combinations described herein include crystalline forms (also known as polymorphs, which include the different crystal packing arrangements of the same elemental composition of a compound), amorphous phases, salts, solvates, and hydrates. In some embodiments, the compounds described herein exist in solvated forms with pharmaceutically acceptable solvents such as water, ethanol, or the like. In other embodiments, the compounds described herein exist in unsolvated form. Solvates contain either stoichiometric or non-stoichiometric amounts of a solvent, and may be formed during the process of crystallization with pharmaceutically acceptable solvents such as water, ethanol, or the like. Hydrates are formed when the solvent is water, or alcoholates are formed when the solvent is alcohol. In addition, the compounds provided herein can exist in unsolvated as well as solvated forms. In general, the solvated forms are considered equivalent to the unsolvated forms for the purposes of the compounds and methods provided herein.

Where a range of values is provided, it is understood that the upper and lower limit, and each intervening value between the upper and lower limit of the range is encompassed within the embodiments.

Some embodiments disclosed herein relate to a compound of Formula (I) or a pharmaceutically acceptable salt thereof:

wherein: B¹ can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group; R¹ can be selected from O⁻, OH, an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; R² can be absent or selected from hydrogen, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl and

wherein R⁶, R⁷ and R⁸ can be independently absent or hydrogen, and n can be 0 or 1; provided that when R¹ is O⁻ or OH, then R² can be absent, hydrogen or

R³ can be selected from hydrogen, halogen, —OR⁹ and —OC(═O)R¹⁰; R⁴ can be selected from halogen, —OR¹¹ and —OC(═O)R¹²; or R³ and R⁴ can both be oxygen atoms and linked together by a carbonyl group; R⁵ can be selected from an optionally substituted C₂₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl and an optionally substituted C₃₋₆ cycloalkyl; or R⁴ and R⁵ together can form —(C₁₋₆ alkyl)-O— or —O—(C₁₋₆ alkyl)-; R⁹ and R¹¹ can be independently hydrogen or an optionally substituted C₁₋₆ alkyl; and R¹⁰ and R¹² can be independently an optionally substituted C₁₋₆ alkyl or an optionally substituted C₃₋₆ cycloalkyl.

The substituents attached to the 2′-carbon can vary. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl. Suitable alkyl groups include, but are not limited to optionally substituted variants of the following: ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In some embodiments, R⁵ can be a substituted C₂₋₆ alkyl. In some embodiments, R⁵ can be an unsubstituted C₂₋₆ alkyl.

In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl or an optionally substituted C₂₋₆ alkynyl. In other embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl. Suitable alkenyl groups include, but are not limited to optionally substituted variants of the following: ethenyl, n-propenyl, isopropenyl, n-butenyl, isobutenyl, tert-butenyl, pentenyl (branched and straight-chained), and hexenyl (branched and straight-chained). The double bond(s) can be at any position(s) within the alkenyl group. The alkenyl group can have one, two, or more than two double bonds. In some embodiments, R⁵ can be a substituted C₂₋₆ alkenyl. In other embodiments, R⁵ can be an unsubstituted C₂₋₆ alkenyl.

In still other embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl. Suitable alkynyl groups include, but are not limited to optionally substituted variants of the following: ethynyl, n-propynyl, isopropynyl, n-butynyl, isobutynyl, tert-butynyl, pentynyl (branched and straight-chained), and hexynyl (branched and straight-chained). The triple bond(s) can be at any position(s) within the alkynyl group. The alkynyl group can have one, two, or more than two triple bonds. In some embodiments, R⁵ can be a substituted C₂₋₆ alkynyl, such as a 2-haloethynyl or 2-(C₁₋₆ alkyl)-ethynyl. In some embodiments, R⁵ can be 2-fluoroethynyl, 2-chloroethynyl, 2-bromoethynyl, 2-iodoethynyl, 2-methylethynyl, 2-ethylethynyl or 2-isopropylethynyl. In some embodiments, R⁵ can be an unsubstituted C₂₋₆ alkynyl.

In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl. Suitable cycloalkyl groups include, but are not limited to optionally substituted variants of the following: cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. In some embodiments, R⁵ can be a substituted C₃₋₆ cycloalkyl. In some embodiments, R⁵ can be an unsubstituted C₃₋₆ cycloalkyl.

In some embodiments, R⁴ can be halogen. For example, R⁴ can be chloro or fluoro. In other embodiments, R⁴ can be —OR¹¹. In some embodiments, when R¹¹ is hydrogen, R⁴ can be a hydroxy group. In still other embodiments, when R¹¹ is an optionally substituted C₁₋₆ alkyl, R⁴ can be an optionally substituted C₁₋₆ alkoxy. Examples of R⁴ being —OR¹¹, wherein R¹¹ can be an optionally substituted C₁₋₆ alkyl include, but are not limited to, are methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy, tert-butoxy, pentoxy (straight-chained or branched) and hexoxy (straight-chained or branched). In yet still other embodiments, R⁴ can be —OC(═O)R¹², wherein R¹² can be an optionally substituted C₁₋₆ alkyl, such as optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In some embodiments, R⁴ can be —OC(═O)R¹², wherein R¹² can be an optionally substituted C₃₋₆ cycloalkyl, such as those described herein.

In some embodiments, R⁴ and R⁵ can together form —(C₁₋₆ alkyl)-O— or —O—(C₁₋₆ alkyl)-. In some embodiments, R⁴ and R⁵ can together form —(C₁₋₆ alkyl)-O—, such as —CH₂—O—, —CH₂CH₂—O—, —CH₂CH₂CH₂—O—, —CH₂CH₂CH₂CH₂—O—, —CH₂CH₂CH₂CH₂CH₂—O— or —CH₂CH₂CH₂CH₂CH₂CH₂—O—. In some embodiments, R⁴ and R⁵ can together form —O—(C₁₋₆ alkyl)-, such as —O—CH₂—, —O—CH₂CH₂—, —O—CH₂CH₂CH₂—, —O—CH₂CH₂CH₂CH₂—, —O—CH₂CH₂CH₂CH₂CH₂— or —O—CH₂CH₂CH₂CH₂CH₂CH₂—. The C₁₋₆ alkyl group can be an optionally substituted C₁₋₆ alkyl, such as optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained).

The substituents attached to the 3′-carbon can vary. In some embodiments, R³ can be hydrogen. In other embodiments, R³ can be halogen. In other embodiments, R³ can be —OR⁹, wherein R⁹ can be hydrogen. In still other embodiments, R³ can be —OR⁹, wherein R⁹ can be an optionally substituted C₁₋₆ alkyl. A non-limiting list of examples of R³ being —OR⁹, wherein R⁹ can be an optionally substituted C₁₋₆ alkyl are methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy and tert-butoxy, pentoxy (straight-chained or branched) and hexoxy (straight-chained or branched). In yet still other embodiments, R³ can be —OC(═O)R¹⁰, wherein R¹⁰ can be an optionally substituted C₁₋₆ alkyl or an optionally substituted C₃₋₆ cycloalkyl. Examples of suitable optionally substituted C₁₋₆ alkyls include optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl pentyl (branched and straight-chained), and hexyl (branched and straight-chained). Examples of suitable optionally substituted C₃₋₆ cycloalkyls include optionally substituted variants of the following: cyclopropyl, cyclobutyl, cyclopentyl and cyclohexyl.

In some embodiments, R³ and R⁴ can both be hydroxy. In still other embodiments, R³ and R⁴ can both be oxygen atoms and linked together by a carbonyl group, for example, —O—C(═O)—O—.

In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl and R⁴ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be a halogen, and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be a halogen, and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be a halogen, and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be a halogen, and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl and R⁴ can be —OR¹¹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be —OR¹¹, and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be —OR¹¹, and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be —OR¹¹, and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be —OR¹¹, and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl and R⁴ can be —OC(═O)R¹². In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be —OC(═O)R¹², and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be —OC(═O)R¹², and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be —OC(═O)R¹², and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkyl, R⁴ can be —OC(═O)R¹², and R³ can be —OC(═O)R¹⁰. In some embodiments, B¹ can be an optionally substituted adenine, an optionally substituted guanine, an optionally substituted thymine, an optionally substituted cytosine, or an optionally substituted uracil in any of the embodiments described in this paragraph.

In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl and R⁴ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be a halogen, and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be a halogen, and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be a halogen, and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be a halogen, and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl and R⁴ can be —OR¹¹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be —OR¹¹, and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be —OR¹¹, and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be —OR¹¹, and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be —OR¹¹, and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl and R⁴ can be —OC(═O)R¹². In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be —OC(═O)R¹², and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be —OC(═O)R¹², and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be —OC(═O)R¹², and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkenyl, R⁴ can be —OC(═O)R¹², and R³ can be —OC(═O)R¹⁰. In some embodiments, B¹ can be an optionally substituted adenine, an optionally substituted guanine, an optionally substituted thymine, an optionally substituted cytosine, or an optionally substituted uracil in any of the embodiments described in this paragraph.

In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl and R⁴ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be a halogen, and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be a halogen, and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be a halogen, and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be a halogen, and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl and R⁴ can be —OR¹¹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be —OR¹¹, and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be —OR¹¹, and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be —OR¹¹, and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be —OR¹¹, and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl and R⁴ can be —OC(═O)R¹². In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be —OC(═O)R¹², and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be —OC(═O)R¹², and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be —OC(═O)R¹², and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₂₋₆ alkynyl, R⁴ can be —OC(═O)R¹², and R³ can be —OC(═O)R¹⁰. In some embodiments, B¹ can be an optionally substituted adenine, an optionally substituted guanine, an optionally substituted thymine, an optionally substituted cytosine, or an optionally substituted uracil in any of the embodiments described in this paragraph.

In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl and R⁴ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be a halogen, and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be a halogen, and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be a halogen, and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be a halogen, and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl and R⁴ can be —OR¹¹. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be —OR¹¹, and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be —OR¹¹, and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be —OR¹¹, and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be —OR¹¹, and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl and R⁴ can be —OC(═O)R¹². In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be —OC(═O)R¹², and R³ can be hydrogen. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be —OC(═O)R¹², and R³ can be a halogen. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be —OC(═O)R¹², and R³ can be —OR⁹. In some embodiments, R⁵ can be an optionally substituted C₃₋₆ cycloalkyl, R⁴ can be —OC(═O)R¹², and R³ can be —OC(═O)R¹⁰. In some embodiments, B¹ can be an optionally substituted adenine, an optionally substituted guanine, an optionally substituted thymine, an optionally substituted cytosine, or an optionally substituted uracil in any of the embodiments described in this paragraph.

In some embodiments, R⁴ and R⁵ can together form —(C₁₋₆ alkyl)-O— or —O—(C₁₋₆ alkyl)-, and R³ can be hydrogen. In some embodiments, R⁴ and R⁵ can together form —(C₁₋₆ alkyl)-O— or —O—(C₁₋₆ alkyl)-, and R³ can be a halogen. In some embodiments, R⁴ and R⁵ can together form —(C₁₋₆ alkyl)-O— or —O—(C₁₋₆ alkyl)-, and R³ can be —OR⁹. In some embodiments, R⁴ and R⁵ can together form —(C₁₋₆ alkyl)-O— or —O—(C₁₋₆ alkyl)-, and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁴ and R⁵ can together form —CH₂—O—, —CH₂CH₂—O—, —CH₂CH₂CH₂—O—, —CH₂CH₂CH₂CH₂—O—, —CH₂CH₂CH₂CH₂CH₂—O— or CH₂CH₂CH₂CH₂CH₂CH₂—O—, and R³ can be hydrogen. In some embodiments, R⁴ and R⁵ can together form —CH₂—O—, —CH₂CH₂—O—, —CH₂CH₂CH₂—O—, —CH₂CH₂CH₂CH₂—O—, —CH₂CH₂CH₂CH₂CH₂—O— or —CH₂CH₂CH₂CH₂CH₂CH₂—O—, and R³ can be a halogen. In some embodiments, R⁴ and R⁵ can together form —CH₂—O—, —CH₂CH₂—O—, —CH₂CH₂CH₂—O—, —CH₂CH₂CH₂CH₂—O—, —CH₂CH₂CH₂CH₂CH₂—O— or —CH₂CH₂CH₂CH₂CH₂CH₂—O—, and R³ can be —OR⁹. In some embodiments, R⁴ and R⁵ can together form —CH₂—O—, —CH₂CH₂—O—, —CH₂CH₂CH₂—O—, —CH₂CH₂CH₂CH₂—O—, —CH₂CH₂CH₂CH₂CH₂—O— or CH₂CH₂CH₂CH₂CH₂CH₂—O—, and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁴ and R⁵ can together form —O—CH₂—, —O—CH₂CH₂—, —O—CH₂CH₂CH₂—, —O—CH₂CH₂CH₂CH₂—, —O—CH₂CH₂CH₂CH₂CH₂— or —O—CH₂CH₂CH₂CH₂CH₂CH₂—, and R³ can be hydrogen. In some embodiments, R⁴ and R⁵ can together form —O—CH₂—, —O—CH₂CH₂—, —O—CH₂CH₂CH₂—, —O—CH₂CH₂CH₂CH₂—, —O—CH₂CH₂CH₂CH₂CH₂— or —O—CH₂CH₂CH₂CH₂CH₂CH₂—, and R³ can be a halogen. In some embodiments, R⁴ and R⁵ can together form —O—CH₂—, —O—CH₂CH₂—, —O—CH₂CH₂CH₂—, —O—CH₂CH₂CH₂CH₂—, —O—CH₂CH₂CH₂CH₂CH₂— or —O—CH₂CH₂CH₂CH₂CH₂CH₂—, and R³ can be —OR⁹. In some embodiments, R⁴ and R⁵ can together form —O—CH₂—, —O—CH₂CH₂—, —O—CH₂CH₂CH₂—, —O—CH₂CH₂CH₂CH₂—, —O—CH₂CH₂CH₂CH₂CH₂— or —O—CH₂CH₂CH₂CH₂CH₂CH₂—, and R³ can be —OC(═O)R¹⁰.

In some embodiments, R⁴ can be a halogen and R³ can be a hydrogen. In some embodiments, R⁴ can be a halogen and R³ can be a halogen. In some embodiments, R⁴ can be a halogen and R³ can be —OR⁹. In some embodiments, R⁴ can be a halogen and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁴ can be —OR¹¹ and R³ can be a hydrogen. In some embodiments, R⁴ can be —OR¹¹ and R³ can be a halogen. In some embodiments, R⁴ can be —OR¹¹ and R³ can be —OR⁹. In some embodiments, R⁴ can be —OR¹¹ and R³ can be —OC(═O)R¹⁰. In some embodiments, R⁴ can be —OC(═O)R¹² and R³ can be a hydrogen. In some embodiments, R⁴ can be —OC(═O)R¹² and R³ can be a halogen. In some embodiments, R⁴ can be —OC(═O)R¹² and R³ can be —OR⁹. In some embodiments, R⁴ can be —OC(═O)R¹² and R³ can be —OC(═O)R¹⁰.

With respect to R², in some embodiments, R² can be absent. In some embodiments, R² can be hydrogen. Those skilled in the art understand that when R² is absent, the oxygen atom that is associated with R² will have a negative charge. In some embodiments, R² can be an optionally substituted heteroaryl. In other embodiments, R² can be an optionally substituted heterocyclyl. In still other embodiments, R² can be an optionally substituted aryl. For example, R² can be an optionally substituted phenyl or an optionally substituted naphthyl. If R² is a substituted phenyl or a substituted naphthyl, the phenyl ring and the naphthyl ring(s) can be substituted one or more times. Suitable substituents that can be present on optionally substituted phenyl and an optionally substituted naphthyl include electron-donating groups and electron-withdrawing groups. In some embodiments, R² can be a substituted phenyl or a substituted naphthyl that is substituted one or more times with a halogen, such as chloro, fluoro, bromo, or iodo. In some embodiments, R² can be a para-substituted phenyl, such as para-chlorophenyl, para-fluorophenyl, para-bromophenyl, or para-iodophenyl. In some embodiments, R² can be a meta-substituted phenyl, such as meta-chlorophenyl, meta-fluorophenyl, meta-bromophenyl, or meta-iodophenyl. In some embodiments, R² can be an ortho-substituted phenyl, such as ortho-chlorophenyl, ortho-fluorophenyl, ortho-bromophenyl, or ortho-iodophenyl. In some embodiments, R² can be a meta-para-disubstituted phenyl, such as meta-para-dichlorophenyl, meta-para-difluorophenyl, meta-para-dibromophenyl, meta-para-diiodophenyl, meta-chloro-para-bromophenyl, meta-bromo-para-chlorophenyl, meta-bromo-para-fluorophenyl, meta-fluoro-para-bromophenyl, meta-chloro-para-fluorophenyl, or meta-fluoro-para-chlorophenyl. In some embodiments, R² can be an ortho-para-disubstituted phenyl, such as ortho-para-dichlorophenyl, ortho-para-diflourophenyl, ortho-para-dibromophenyl, ortho-para-diiodophenyl, ortho-chloro-para-bromophenyl, ortho-bromo-para-chlorophenyl, ortho-bromo-para-fluorophenyl, ortho-fluoro-para-bromophenyl, ortho-chloro-para-fluorophenyl, or ortho-fluoro-para-chlorophenyl. In some embodiments, R² can be an ortho-meta-disubstituted phenyl, such as ortho-meta-dichlorophenyl, ortho-meta-diflourophenyl, ortho-meta-dibromophenyl, ortho-meta-diiodophenyl, ortho-chloro-meta-bromophenyl, ortho-bromo-meta-chlorophenyl, ortho-bromo-meta-fluorophenyl, ortho-fluoro-meta-bromophenyl, ortho-chloro-meta-fluorophenyl, or ortho-fluoro-meta-chlorophenyl. In other embodiment, R² can be an unsubstituted phenyl or an unsubstituted naphthyl.

In some embodiments, R² can be absent or hydrogen, and R¹ can be OH or O⁻. In some embodiment,

can be a monothiophosphate. In other embodiments, R² can be

wherein R⁶, R⁷ and R⁸ can be independently absent or hydrogen, and n can be 0 or 1. In some embodiments, n can be 0. In other embodiments, n can be 1. Those skilled in the art understand when n is 0, R² can be an α-thiodiphosphate. Similarly, those skilled in the art understand when n is 1, R² can be an α-thiotriphosphate. In some embodiments, at least one of R⁶, R⁷ and R⁸ can be absent. In other embodiments, at least one of R⁶, R⁷ and R⁸ can be hydrogen. In some embodiments, R⁷ and R⁸ can be absent. In other embodiments, R⁷ and R⁸ can be hydrogen. In some embodiments, R⁶, R⁷ and R⁸ can be absent. In some embodiments, R⁶, R⁷ and R⁸ can be hydrogen. Those skilled in the art understand that when any of R⁶, R⁷ and R⁸ are absent the oxygen atom to which R⁶, R⁷ and R⁸ are associated with can have a negative charge. For example, when R⁷ is absent, the oxygen atom to which R⁷ is associated with can be O⁻. Depending upon the substituents attached to each phosphorus atoms, one or more the phosphorus atoms can be a chiral center. For example, when n is 1, the alpha-phosphorus (the phosphorus nearest to the pentose ring) can be a chiral center. In some embodiments, the alpha-phosphorus can be a (R)-stereocenter. In other embodiments, the alpha-phosphorus can be a (S)-stereocenter.

In some embodiments, R¹ can be O⁻. In other embodiments, R¹ can be OH. In still other embodiments, R¹ can be an optionally substituted N-linked α-amino acid. In yet still other embodiments, R¹ can be an optionally substituted N-linked α-amino acid ester derivative. Various amino acids and amino acid ester derivatives can be used, including those described herein. Suitable amino acids include, but are not limited to, alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, tyrosine, arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Additional suitable amino acids include, but are not limited to, alpha-ethyl-glycine, alpha-propyl-glycine and beta-alanine. Examples of an N-linked amino acid ester derivatives include, but are not limited to, an ester derivatives of any of the following amino acids: alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, tyrosine, arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Additional examples of N-linked amino acid ester derivatives include, but are not limited to, an ester derivative of any of the following amino acids: alpha-ethyl-glycine, alpha-propyl-glycine and beta-alanine.

In an embodiment, R¹ can be an ester derivative of alanine. In an embodiment, R¹ can be selected from alanine methyl ester, alanine ethyl ester, alanine isopropyl ester, alanine cyclohexyl ester, alanine neopentyl ester, valine isopropyl ester, isoleucine isopropyl ester, methionine isopropyl ester, and leucine isopropyl ester. In some embodiments, R¹ can be 2-aminobutane isopropyl ester. In some embodiments, the optionally substituted N-linked amino acid or the optionally substituted N-linked amino acid ester derivative can be in the L-configuration. In other embodiments, the optionally substituted N-linked amino acid or the optionally substituted N-linked amino acid ester derivative can be in the D-configuration.

In some embodiments, when R¹ is an optionally substituted N-linked α-amino acid or an optionally substituted N-linked α-amino acid ester derivative, then R² can be selected from optionally substituted aryl, an optionally substituted heteroaryl and an optionally substituted heterocyclyl. In some embodiments, when R¹ is an optionally substituted N-linked α-amino acid ester derivative, then R² can be an optionally substituted aryl. In other embodiments, when R¹ is an optionally substituted N-linked α-amino acid ester derivative, then R² can be an optionally substituted heteroaryl. In still other embodiments, when R¹ is an optionally substituted N-linked α-amino acid ester derivative, then R² can be an optionally substituted heterocyclyl.

In some embodiments, R¹ can have the structure

wherein R¹³ can be selected from hydrogen, an optionally substituted C₁₋₆-alkyl, an optionally substituted C₃₋₆ cycloalkyl, an optionally substituted aryl, an optionally substituted aryl(C₁₋₆ alkyl) and an optionally substituted C₁₋₆ haloalkyl; and R¹⁴ can be selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₁₋₆ haloalkyl, an optionally substituted C₃₋₆ cycloalkyl, an optionally substituted C₆ aryl, an optionally substituted C₁₀ aryl and an optionally substituted aryl(C₁₋₆ alkyl); and R¹⁵ can be hydrogen or an optionally substituted C₁₋₄-alkyl; or R¹⁴ and R¹⁵ can be taken together to form an optionally substituted C₃₋₆ cycloalkyl.

When R¹ has the structure shown above, R¹⁴ can be an optionally substituted C₁₋₆-alkyl. Examples of suitable optionally substituted C₁₋₆-alkyls include optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). When R¹⁴ is substituted, R¹⁴ can be substituted with one or more substituents selected from N-amido, mercapto, alkylthio, an optionally substituted aryl, hydroxy, an optionally substituted heteroaryl, O-carboxy, and amino. In some embodiment, R¹⁴ can be an unsubstituted C₁₋₆-alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In an embodiment, R¹⁴ can be methyl.

As to R¹³, in some embodiments, R³ can be an optionally substituted C₁₋₆ alkyl. Examples of optionally substituted C₁₋₆-alkyls include optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In some embodiments, R¹³ can be methyl or isopropyl. In some embodiments, R¹³ can be ethyl or neopentyl. In other embodiments, R¹³ can be an optionally substituted C₃₋₆ cycloalkyl. Examples of optionally substituted C₃₋₆ cycloalkyl include optionally substituted variants of the following: cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. In an embodiment, R¹³ can be an optionally substituted cyclohexyl. In still other embodiments, R¹³ can be an optionally substituted aryl, such as phenyl and naphthyl. In yet still other embodiments, R¹³ can be an optionally substituted aryl(C₁₋₆ alkyl). In some embodiments, R¹³ can be an optionally substituted benzyl. In some embodiments, R¹³ can be an optionally substituted C₁₋₆ haloalkyl, for example, CF₃.

In some embodiments, R¹⁵ can be hydrogen. In other embodiments, R¹⁵ can be an optionally substituted C₁₋₄-alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl and tert-butyl. In an embodiment, R¹⁵ can be methyl. In some embodiments, R¹⁴ and R¹⁵ can be taken together to form an optionally substituted C₃₋₆ cycloalkyl. Examples of optionally substituted C₃₋₆ cycloalkyl include optionally substituted variants of the following: cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. Depending on the groups that are selected for R¹⁴ and R¹⁵, the carbon to which R¹⁴ and R¹⁵ are attached may be a chiral center. In some embodiment, the carbon to which R¹⁴ and R¹⁵ are attached may be a (R)-chiral center. In other embodiments, the carbon to which R¹⁴ and R¹⁵ are attached may be a (S)-chiral center.

Examples of suitable

groups include the following:

Various optionally substituted heterocyclic bases can be attached to the pentose ring. In some embodiments, one or more of the amine and/or amino groups may be protected with a suitable protecting group. For example, an amino group may be protected by transforming the amine and/or amino group to an amide or a carbamate. In some embodiments, an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with one or more protected amino groups can have one of the following structures:

wherein: R^(A2) can be selected from hydrogen, halogen and NHR^(J2), wherein R^(J2) can be selected from hydrogen, —C(═O)R^(K2) and —C(═O)OR^(L2); R^(B2) can be halogen or NHR^(W2), wherein R^(W2) is selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₃₋₈ cycloalkyl, —C(═O)R^(M2) and —C(═O)OR^(N2); R^(C2) can be hydrogen or NHR^(O2), wherein R^(O2) can be selected from hydrogen, —C(═O)R^(P2) and —C(═O)OR^(Q2); R^(D2) can be selected from hydrogen, halogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl and an optionally substituted C₂₋₆ alkynyl; R^(E2) can be selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₃₋₈ cycloalkyl, —C(═O)R^(R2) and —C(═O)OR^(S2); R^(F2) and R^(X2) can be independently selected from hydrogen, halogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl and an optionally substituted C₂₋₆ alkynyl; Y² can be N (nitrogen) or CR^(I2), wherein R^(I2) can be selected from hydrogen, halogen, an optionally substituted C₁₋₆-alkyl, an optionally substituted C₂₋₆-alkenyl and an optionally substituted C₂₋₆-alkynyl; R^(G2) can be an optionally substituted C₁₋₆ alkyl; R^(H2) can be hydrogen or NHR^(T2), wherein R^(T2) can be independently selected from hydrogen, —C(═O)R^(U2) and C(═O)OR^(V2), R^(K2), R^(L2), R^(M2), R^(N2), R^(P2), R^(Q2) R^(R2), R^(S2), R^(U2) and R^(V2) can be independently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₆ cycloalkyl, C₃₋₆ cycloalkenyl, C₆₋₁₀ aryl, heteroaryl, heteroalicyclyl, aryl(C₁₋₆ alkyl), heteroaryl(C₁₋₆ alkyl) and heteroalicyclyl(C₁₋₆ alkyl); and R^(Y2) can be an optionally substituted C₁₋₆ alkyl or an optionally substituted C₃₋₆ cycloalkyl. In some embodiments, the structures shown above can be modified by replacing one or more hydrogens with substituents selected from the list of substituents provided for the definition of “substituted.” Suitable optionally substituted C₁₋₆ alkyl groups that can be present on an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with one or more protected amino groups are described herein, and include, optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In some embodiments, B¹ can be a naturally occurring nucleobase. In other embodiments, B¹ can be a non-naturally occurring nucleobase. In some embodiments, B¹ can be selected from adenine, guanine, thymine, cytosine and uracil.

In some embodiments, R^(B2) can be NH₂. In other embodiments, R^(E2) can be hydrogen. In some embodiments, B¹ can be

In other embodiments, B¹ can be

In some embodiments, B¹ can be

In some embodiments, B¹ can be

In some embodiments, R^(W2) can be hydrogen. In still other embodiments, B¹ can be

In some embodiments, B¹ can be

In yet still other embodiments, B¹ can be

In some embodiments, B¹ can be

In other embodiments, B¹ can be

In still other embodiments, B¹ can be

wherein R^(X2) is hydrogen.

In some embodiments, R⁵ cannot be an optionally substituted C₂₋₆ alkyl. In some embodiments, R⁴ cannot be halogen. In some embodiments, when R⁴ is halogen, then R³ cannot be hydrogen or halogen. In some embodiments, when R⁴ is halogen, then R³ can be —OR⁹ or —OC(═O)R¹⁰. In some embodiments, R² cannot be hydrogen. In some embodiments, when R² is hydrogen, then R¹ cannot be O⁻ or OH. In some embodiments, when R² is hydrogen, then R¹ can be an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative. In some embodiments, when R¹ is O⁻ or OH, then R² cannot be

In some embodiments, at least one of R³ and R⁴ cannot be hydroxy. For example, R³ cannot be hydroxy, R⁴ cannot be hydroxy, or both of R³ and R⁴ cannot be hydroxy.

Some embodiments disclosed herein relate to a compound of Formula (I) or a pharmaceutically acceptable salt thereof, wherein: B¹ can be an optionally substituted heterocyclic base as described in paragraph [0110]; R¹ can be selected from O⁻, OH, an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; R² can be absent or selected from hydrogen, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl and

wherein R⁶, R⁷ and R⁸ can be independently absent or hydrogen, and n can be 0 or 1; provided that when R¹ is O⁻ or OH, then R² can be absent, hydrogen or

R³ can be selected from hydrogen, halogen and —OR⁹; R⁴ can be halogen or —OR¹¹; R⁵ can be selected from an optionally substituted C₂₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl and an optionally substituted C₂₋₆ alkynyl; and R⁹ and R¹¹ can be independently hydrogen or an optionally substituted C₁₋₆ alkyl.

Some embodiments disclosed herein relate to a compound of Formula (I) or a pharmaceutically acceptable salt thereof, wherein: B¹ can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group selected from

R¹ can be selected from O⁻, OH, an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; R² can be absent or selected from hydrogen, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl and

wherein R⁶, R⁷ and R⁸ can be independently absent or hydrogen, and n can be 0 or 1; provided that when R¹ is O⁻ or OH, then R² can be absent, hydrogen or

R³ can be selected from hydrogen, halogen and —OR⁹; R⁴ can be halogen or —OR¹¹; R⁵ can be selected from an optionally substituted C₂₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl and an optionally substituted C₂₋₆ alkynyl; and R⁹ and can be independently hydrogen or an optionally substituted C₁₋₆ alkyl.

Some embodiments relate to a compound of Formula (I) or a pharmaceutically acceptable salt thereof, wherein: B¹ can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group; R¹ can be selected from O⁻, OH, an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; R² can be absent or selected from hydrogen, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl and

wherein R⁶, R⁷ and R⁸ can be independently absent or hydrogen, and n can be 0 or 1; provided that when R¹ is O⁻ or OH, then R² can be absent, hydrogen or

R³ can be selected from hydrogen, halogen, —OR⁹ and —OC(═O)R¹⁰; R⁴ can be selected from halogen, —OR¹¹ and —OC(═O)R¹²; or R³ and R⁴ can both be oxygen atoms and linked together by a carbonyl group; R⁵ can be an optionally substituted C₂₋₆ alkenyl or an optionally substituted C₂₋₆ alkynyl; R⁹ and can be independently hydrogen or an optionally substituted C₁₋₆ alkyl; and R¹⁹ and R¹² can be independently an optionally substituted C₁₋₆ alkyl or an optionally substituted C₃₋₆ cycloalkyl.

In some embodiments, a compound of Formula (I) can be a single diastereomer. In other embodiments, a compound of Formula (I) can be a mixture of diastereomers. In some embodiments, a compound of Formula (I) can be a 1:1 mixture of two diastereomers. In some embodiments, a compound of Formula (I) can be diasteriometrically enriched (for example, one diastereomer can be present at a concentration of >55%, ≧75%, ≧80%, ≧90%, ≧95%, ≧98%, or ≧99% as compared to the total concentration of the other diastereomers).

Examples of compounds of Formula (I) include, but are not limited to the following:

or a pharmaceutical acceptable salt of the foregoing.

Additional examples of compounds of Formula (I) include the following:

or a pharmaceutical acceptable salt of the foregoing.

In some embodiments, neutralizing the charge on the thiophosphate group may facilitate the penetration of the cell membrane by a compound of Formula (I), or a pharmaceutically acceptable salt thereof, by making the compound more lipophilic compared to a thionucleotide having a comparable structure with one or more charges present on the phosphate. Once absorbed and taken inside the cell, the groups attached to the thiophosphate can be easily removed by esterases, proteases, or other enzymes. In some embodiments, the groups attached to the thiophosphate can be removed by simple hydrolysis. Inside the cell, the thio-monophosphate thus released may then be metabolized by cellular enzymes to the thio-diphosphate or the active thio-triphosphate. Furthermore, in some embodiments, varying the substituents on a compound described herein, such as compound of Formula (I), can help maintain the efficacy of such the compound by reducing undesirable effects, such as isomerization.

In some embodiments, the phosphorylation of a thio-monophosphate of a compound of Formula (I), or pharmaceutically acceptable salt thereof, can be stereoselective. For example, a thio-monophosphate of a compound of Formula (I) can be phosphorylated to give an alpha-thiodiphosphate and/or an alpha-thiotriphosphate compound that can be enriched in the (R) or (S) diastereomer with respect to the 5′-O-phosphorous atom. For example, one of the (R) and (S) configuration with respect to the 5′-O-phosphorous atom of the alpha-thiodiphosphate and/or the alpha-thiotriphosphate compound can be present in an amount >50%, ≧75%, ≧90%, ≧95% or ≧99% compared to the amount of the other of the (R) or (S) configuration with respect to the 5′-O-phosphorous atom. In some embodiments, phosphorylation of a compound of Formula (I), or pharmaceutically acceptable salt thereof, can result in the formation of a compound that has the (R)-configuration at the 5′-O-phosphorous atom. In some embodiments, phosphorylation of a compound of Formula (I), or pharmaceutically acceptable salt thereof, can result in formation of a compound that has the (S)-configuration at the 5′-O-phosphorous atom.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can act as a chain terminator of HCV replication. For example, compounds of Formula (I) can contain a moiety at the 2′-carbon position such that once the compound is incorporated into an RNA chain of HCV no further elongation is observed to occur. For example, a compound of Formula (I) can contain a 2′-carbon modification wherein R⁵ is a non-hydrogen group selected from an optionally substituted C₂₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl and an optionally substituted C₂₋₆ alkynyl.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have increased metabolic and/or plasma stability. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be more resistant to hydrolysis and/or more resistant to enzymatic transformations. For example, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have increased metabolic stability, increased plasma stability, can be more resistant to hydrolysis and/or can be more resistant to enzymatic transformations compared to a compound that is identical in structure but for having a phosphate attached to the 5′-carbon of the ribose ring. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have improved properties. In previous studies, replacing a sulfur with an oxygen on the alpha-phosphate of a nucleotide phosphoroamidate has resulted in more than a 1000-fold decrease in potency. See Venkatachalam et al. European Journal of Medicinal Chemistry (2004) 39:665-683. A non-limiting list of example properties include, but are not limited to, increased biological half-life, increased bioavailability, increase potency, a sustained in vivo response, increased dosing intervals, decreased dosing amounts, decreased cytotoxicity, reduction in required amounts for treating disease conditions, reduction in viral load, reduction in time to seroconversion (i.e., the virus becomes undetectable in patient serum), increased sustained viral response, a reduction of morbidity or mortality in clinical outcomes, increased subject compliance, decreased liver conditions (such as liver fibrosis, liver cirrohis and/or liver cancer), and compatibility with other medications. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have a biological half-life of greater than 24 hours. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have a biological half-life in the range of about 40 hours to about 46 hours. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have a biological half-life greater than a compound that has a phosphate attached to the 5′-carbon of the ribose ring (for example, a compound that is identical in structure but for having a phosphate attached to the 5′-carbon of the ribose ring). In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have more potent antiviral activity (for example, a lower EC₅₀ in an HCV replicon assay) as compared to the current standard of care.

Additionally, in some embodiments, the presence of a phosphorothioamidate in a compound of Formula (I) can increase the stability of the compound by inhibiting its degradation. Also, in some embodiments, the presence of a phosphorothioamidate can make the compound more resistant to cleavage in vivo and provide sustained, extended efficacy. In some embodiments, a phosphorothioamidate can facilitate the penetration of the cell membrane by a compound of Formula (I) by making the compound more lipophilic.

Synthesis

Compounds of Formula (I) and those described herein may be prepared in various ways. General synthetic routes to the compound of Formula (I), and some examples of starting materials used to synthesize the compounds of Formula (I) are shown in Scheme 1, and described herein. The routes shown and described herein are illustrative only and are not intended, nor are they to be construed, to limit the scope of the claims in any manner whatsoever. Those skilled in the art will be able to recognize modifications of the disclosed syntheses and to devise alternate routes based on the disclosures herein; all such modifications and alternate routes are within the scope of the claims.

One method for forming a compound of Formula (I) is shown in Scheme 1. In Scheme 1, R^(3A), R^(4A), R^(5A) and B^(1A) can be the same as R³, R⁴, R⁵ and B¹ as described herein for Formula (I); and R¹ and R² can be the same as described herein for Formula (I). As shown in Scheme 1, a compound of Formula (A) can be reacted with a compound having the formula R²O—P(═S)(R¹)—Cl to form a compound of Formula (I).

To reduce the formation of side products, one or more the groups attached to the pentose ring can be protected with one or more suitable protecting groups. As an example, if R^(3A) and/or R^(4A) is/are hydroxy group(s), the hydroxy group(s) can be protected with suitable protecting groups, such as triarylmethyl and/or silyl groups. Examples of triarylmethyl groups include but are not limited to, trityl, monomethoxytrityl (MMTr), 4,4′-dimethoxytrityl (DMTr), 4,4′,4″-trimethoxytrityl (TMTr), 4,4′,4″-tris-(benzoyloxy)trityl (TBTr), 4,4′,4″-tris(4,5-dichlorophthalimido)trityl (CPTr), 4,4′,4″-tris(levulinyloxy)trityl (TLTr), p-anisyl-1-naphthylphenylmethyl, di-o-anisyl-1-naphthylmethyl, p-tolyldipheylmethyl, 3-(imidazolylmethyl)-4,4′-dimethoxytrityl, 9-phenylxanthen-9-yl (Pixyl), 9-(p-methoxyphenyl) xanthen-9-yl (Mox), 4-decyloxytrityl, 4-hexadecyloxytrityl, 4,4′-dioctadecyltrityl, 9-(4-octadecyloxyphenyl) xanthen-9-yl, 1,1′-bis-(4-methoxyphenyl)-1′-pyrenylmethyl, 4,4′,4″-tris-(tert-butylphenyl) methyl (TTTr) and 4,4′-di-3,5-hexadienoxytrityl. Examples of suitable silyl groups are described herein. Alternatively, R^(3A) and/or R^(4A) can be protected by a single achiral or chiral protecting group, for example, by forming an orthoester, a cyclic acetal or a cyclic ketal. Suitable orthoesters include methoxymethylene acetal, ethoxymethylene acetal, 2-oxacyclopentylidene orthoester, dimethoxymethylene orthoester, 1-methoxyethylidene orthoester, 1-ethoxyethylidene orthoester, methylidene orthoester, phthalide orthoester 1,2-dimethoxyethylidene orthoester, and alpha-methoxybenzylidene orthoester; suitable cyclic acetals include methylene acetal, ethylidene acetal, t-butylmethylidene acetal, 3-(benzyloxy)propyl acetal, benzylidene acetal, 3,4-dimethoxybenzylidene acetal and p-acetoxybenzylidene acetal; and suitable cyclic ketals include 1-t-butylethylidene ketal, 1-phenylethylidene ketal, isopropylidene ketal, cyclopentylidene ketal, cyclohexylidene ketal, cycloheptylidene ketal and 1-(4-methoxyphenyl)ethylidene ketal.

If desired, any —NH and/or NH₂ groups present on the B^(1A) can also be protected with one or more suitable protecting groups. Examples of suitable protecting groups include triarylmethyl groups and silyl groups. Examples of silyl groups include, but are not limited to, trimethylsilyl (TMS), tert-butyldimethylsilyl (TBDMS), triisopropylsilyl (TIPS), tert-butyldiphenylsilyl (TBDPS), tri-iso-propylsilyloxymethyl and [2-(trimethylsilyl)ethoxy]methyl.

Suitable thiophosphorochloridates can be synthetically prepared. An example of a general structure of a thiophosphorochloridate is shown in Scheme 1. In some embodiments, the thiophosphorochloridate can be coupled to a compound of Formula (A). In some embodiments, to facilitate the coupling, a Grignard reagent can be used. Suitable Grignard reagents are known to those skilled in the art and include, but are not limited to, alkylmagnesium chlorides and alkylmagnesium bromides. In other embodiments, the thiophosphorochloridate can be added to a compound of Formula (A) using a base. Suitable bases are known to those skilled in the art. Examples of bases include, but are not limited to, an amine base, such as an alkylamine (including mono-, di- and tri-alkylamines (e.g., triethylamine)), optionally substituted pyridines (e.g. collidine) and optionally substituted imidazoles (e.g., N-methylimidazole)).

As described herein, in some embodiments, R³ and R⁴ can be both oxygen atoms linked together by a carbonyl groups. The —O—C(═O)—O— group can be formed using methods known to those skilled in the art. For example, a compound of Formula (I), wherein R³ and R⁴ are both hydroxy groups, can be treated with 1,1′-carbonyldiimidazole (CDI).

In some embodiments, R³ and/or R⁴ can be —OC(═O)R¹⁰ and —OC(═O)R¹², respectively. The —OC(═O)R¹⁰ and —OC(═O)R¹² groups can be formed at the 2′- and 3′-positions using various methods known to those skilled in the art. As an example, a compound of Formula (I), wherein R³ and R⁴ are both hydroxy groups, can be treated with an alkyl anhydride (e.g., acetic anhydride and propionic anhydride) or an alkyl acid chloride (e.g., acetylchloride). If desired, a catalyst can be used to facilitate the reaction. An example of suitable catalyst is 4-dimethylaminopyridine (DMAP). Alternatively, the —OC(═O)R¹⁰ and —OC(═O)R¹² groups can be formed at the 2′- and 3′-positions by reacting an alkyl acid (e.g. acetic acid and propionic acid) in the presences of a carbodiimide or a coupling reagent. Examples of carbodiimides include, but are not limited to, N,N′-dicyclohexylcarbodiimide (DCC), N,N′-diisopropylcarbodiimide (DIC) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC).

As described herein, B^(1A) can include a carbamate and/or an amide. Those skilled in the art know methods for forming a carbamate and/or an amide on B^(1A). In some embodiments, the carbamate can be formed using 1,1′-carbonyldiimidazole and an alcohol.

B^(1A) can be added to the pentose ring using various methods known to those skilled in the art. In some embodiments, a compound of Formula (B) can be reacted with a nitrogenous base. In some embodiments, R^(3A), R^(4A), R^(5A) and B^(1A) of a compound of Formula (B) can be the same as disclosed herein, with respect to R³, R⁴, R⁵ and B¹; and PG¹ can be an appropriate protecting group. In some embodiments, PG¹ can be p-nitrobenzyl group. In some embodiments, any hydroxy groups attached to the pentose ring can be protected with one or more suitable protecting groups. In some embodiments, any hydroxy groups attached to the pentose ring can be protected with benzoyl groups. Examples of nitrogenous bases include an optionally substituted heterocyclic bases described herein, wherein the nitrogen atom (—N) connected to the pentose ring is —NH. If desired, any —NH and/or NH₂ groups present on the nitrogenous base can be protected with one or more suitable protecting groups. Suitable protecting groups are described herein. In some embodiments, the nitrogenous base can be added via a coupling reaction in the presence of a Lewis acid or TMSOTf. Suitable Lewis acids are known to those skilled in the art.

Various methods can be used to make a compound of Formula (I), wherein R¹ is

For example, a thiophosphorochloridate having the general formula of (P(═S)Cl₃) can be transformed into a phosphorus reagent having the general formula, P(═S)LG₃, wherein each LG can be amine-based leaving group. In some embodiments, each LG can be a triazole. The phosphorus reagent having the general formula, P(═S)LG₃, can be reacted with a compound of Formula (I). Using a suitable pyrophosphorylation reagent, the β and γ phosphates can be added. An example of a suitable pyrophosphorylation reagent is tris(tetrabutylammonium) hydrogen pyrophosphate.

During the synthesis of any of the compounds described herein, if desired, any hydroxy groups attached to the pentose ring, and any —NH and/or NH₂ groups present on the B^(1A) can be protected with one or more suitable protecting groups. Suitable protecting groups are described herein. Those skilled in the art will appreciate that groups attached to the pentose ring and any —NH and/or NH₂ groups present on the B^(1A) can be protected with various protecting groups, and any protecting groups present can be exchanged for other protecting groups. The selection and exchange of the protecting groups is within the skill of those of ordinary skill in the art. Any protecting group(s) can also be removed by methods known in the art, for example, with an acid (e.g., a mineral or an organic acid), a base or a fluoride source.

Pharmaceutical Compositions

Some embodiments described herein relates to a pharmaceutical composition, that can include a therapeutically effective amount of one or more compounds described herein (e.g., a compound of Formula (I)), or a pharmaceutically acceptable salt thereof) and a pharmaceutically acceptable carrier, diluent, excipient or combination thereof. In some embodiments, the pharmaceutical composition can include a single diastereomer of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, (for example, a single diastereomer is present in the pharmaceutical composition at a concentration of greater than 99% compared to the total concentration of the other diastereomers). In other embodiments, the pharmaceutical composition can include a mixture of diastereomers of a compound of Formula (I), or a pharmaceutically acceptable salt thereof. For example, the pharmaceutical composition can include a concentration of one diastereomer of >50%, ≧60%, ≧70%, ≧80%, ≧90%, ≧95%, or ≧98%, as compared to the total concentration of the other diastereomers. In some embodiments, the pharmaceutical composition includes a 1:1 mixture of two diastereomers of a compound of Formula (I), or a pharmaceutically acceptable salt thereof

The term “pharmaceutical composition” refers to a mixture of one or more compounds disclosed herein with other chemical components, such as diluents or carriers. The pharmaceutical composition facilitates administration of the compound to an organism. Pharmaceutical compositions can also be obtained by reacting compounds with inorganic or organic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid and salicylic acid. Pharmaceutical compositions will generally be tailored to the specific intended route of administration.

The term “physiologically acceptable” defines a carrier, diluent or excipient that does not abrogate the biological activity and properties of the compound.

As used herein, a “carrier” refers to a compound that facilitates the incorporation of a compound into cells or tissues. For example, without limitation, dimethyl sulfoxide (DMSO) is a commonly utilized carrier that facilitates the uptake of many organic compounds into cells or tissues of a subject.

As used herein, a “diluent” refers to an ingredient in a pharmaceutical composition that lacks pharmacological activity but may be pharmaceutically necessary or desirable. For example, a diluent may be used to increase the bulk of a potent drug whose mass is too small for manufacture and/or administration. It may also be a liquid for the dissolution of a drug to be administered by injection, ingestion or inhalation. A common form of diluent in the art is a buffered aqueous solution such as, without limitation, phosphate buffered saline that mimics the composition of human blood.

As used herein, an “excipient” refers to an inert substance that is added to a pharmaceutical composition to provide, without limitation, bulk, consistency, stability, binding ability, lubrication, disintegrating ability etc., to the composition. A “diluent” is a type of excipient.

The pharmaceutical compositions described herein can be administered to a human patient per se, or in pharmaceutical compositions where they are mixed with other active ingredients, as in combination therapy, or carriers, diluents, excipients or combinations thereof. Proper formulation is dependent upon the route of administration chosen. Techniques for formulation and administration of the compounds described herein are known to those skilled in the art.

The pharmaceutical compositions disclosed herein may be manufactured in a manner that is itself known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or tableting processes. Additionally, the active ingredients are contained in an amount effective to achieve its intended purpose. Many of the compounds used in the pharmaceutical combinations disclosed herein may be provided as salts with pharmaceutically compatible counterions.

Multiple techniques of administering a compound exist in the art including, but not limited to, oral, rectal, topical, aerosol, injection and parenteral delivery, including intramuscular, subcutaneous, intravenous, intramedullary injections, intrathecal, direct intraventricular, intraperitoneal, intranasal and intraocular injections.

One may also administer the compound in a local rather than systemic manner, for example, via injection of the compound directly into the infected area, often in a depot or sustained release formulation. Furthermore, one may administer the compound in a targeted drug delivery system, for example, in a liposome coated with a tissue-specific antibody. The liposomes will be targeted to and taken up selectively by the organ.

The compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may for example comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. The pack or dispenser may also be accompanied with a notice associated with the container in form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the drug for human or veterinary administration. Such notice, for example, may be the labeling approved by the U.S. Food and Drug Administration for prescription drugs, or the approved product insert. Compositions that can include a compound described herein formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.

Methods of Use

Some embodiments disclosed herein relate to a method of treating and/or ameliorating a disease or condition that can include administering to a subject a therapeutically effective amount of one or more compounds described herein, such as a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound described herein, or a pharmaceutically acceptable salt thereof

Some embodiments disclosed herein relate to a method of ameliorating or treating a neoplastic disease that can include administering to a subject suffering from a neoplastic disease a therapeutically effective amount of one or more compounds described herein (e.g., a compound of Formula (I)), or a pharmaceutically acceptable salt thereof), or a pharmaceutical composition that includes a compound described herein, or a pharmaceutically acceptable salt thereof. In some embodiments, the neoplastic disease can be cancer. In some embodiments, the neoplastic disease can be a tumor such as a solid tumor. In an embodiment, the neoplastic disease can be leukemia. Exemplary leukemias include, but are not limited to, acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML) and juvenile myelomonocytic leukemia (JMML).

Some embodiments disclosed herein relate to a method of inhibiting the growth of a tumor that can include administering to a subject having a tumor a therapeutically effective amount of one or more compounds described herein (for example, a compound of Formula (I)), or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof

Other embodiments disclosed herein relates to a method of ameliorating or treating a viral infection that can include administering to a subject suffering from a viral infection a therapeutically effective amount of one or more compounds described herein (for example, a compound of Formula (I)), or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof. In some embodiments, the viral infection can be caused by a virus selected from an adenovirus, an Alphaviridae, an Arbovirus, an Astrovirus, a Bunyaviridae, a Coronaviridae, a Filoviridae, a Flaviviridae, a Hepadnaviridae, a Herpesviridae, an Alphaherpesvirinae, a Betaherpesvirinae, a Gammaherpesvirinae, a Norwalk Virus, an Astroviridae, a Caliciviridae, an Orthomyxoviridae, a Paramyxoviridae, a Paramyxoviruses, a Rubulavirus, a Morbillivirus, a Papovaviridae, a Parvoviridae, a Picornaviridae, an Aphthoviridae, a Cardioviridae, an Enteroviridae, a Coxsackie virus, a Polio Virus, a Rhinoviridae, a Phycodnaviridae, a Poxviridae, a Reoviridae, a Rotavirus, a Retroviridae, an A-Type Retrovirus, an Immunodeficiency Virus, a Leukemia Viruses, an Avian Sarcoma Viruses, a Rhabdoviruses, a Rubiviridae, a Togaviridae an Arenaviridae and/or a Bornaviridae. In some embodiments, the viral infection can be a hepatitis C viral (HCV) infection. In still other embodiments, the viral infection can be HIV.

Some embodiments disclosed herein relate to methods of ameliorating and/or treating a viral infection that can include contacting a cell infected with the virus with an effective amount of one or more compounds described herein, or a pharmaceutically acceptable salt of a compound described herein, or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds described herein, or a pharmaceutically acceptable salt of a compound described herein, in the manufacture of a medicament for ameliorating and/or treating a viral infection that can include contacting a cell infected with the virus with an effective amount of said compound(s). Still other embodiments described herein relate to one or more compounds described herein, or a pharmaceutically acceptable salt of a compound described herein, that can be used for ameliorating and/or treating a viral infection by contacting a cell infected with the virus with an effective amount of said compound(s). In some embodiments, the compound can be a compound of Formula (I), or a pharmaceutical acceptable salt thereof. In other embodiments, the compound can be a mono-, di- and/or tri-phosphate of a compound of Formula (I), or a pharmaceutically acceptable salt of the foregoing. In some embodiments, the virus can be a HCV virus.

Some embodiments disclosed herein relate to methods of inhibiting replication of a virus that can include contacting a cell infected with the virus with an effective amount of one or more compounds described herein, or a pharmaceutically acceptable salt of a compound described herein, or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds described herein, or a pharmaceutically acceptable salt of a compound described herein, in the manufacture of a medicament for inhibiting replication of a virus that can include contacting a cell infected with the virus with an effective amount of said compound(s). Still other embodiments described herein relate to a compound described herein, or a pharmaceutically acceptable salt of a compound described herein, that can be used for inhibiting replication of a virus by contacting a cell infected with the virus with an effective amount of said compound(s). In some embodiments, the compound can be a compound of Formula (I), or a pharmaceutical acceptable salt thereof. In other embodiments, the compound can be a mono-, di- and/or tri-phosphate of a compound of Formula (I), or a pharmaceutically acceptable salt of the foregoing. In some embodiments, the virus can be a HCV virus.

HCV is an enveloped positive strand RNA virus in the Flaviviridae family. There are various nonstructural proteins of HCV, such as NS2, NS3, NS4, NS4A, NS4B, NS5A, and NS5B. NS5B is believed to be an RNA-dependent RNA polymerase involved in the replication of HCV RNA.

Some embodiments described herein relate to a method of inhibiting NS5B polymerase activity that can include contacting a cell (for example, a cell infected with HCV) with an effective amount of a compound of Formula (I), or a pharmaceutical acceptable salt thereof. Some embodiments described herein relate to a method of inhibiting NS5B polymerase activity that can include administering a cell (for example, a cell infected with HCV) with an effective amount of a compound of Formula (I), or a pharmaceutical acceptable salt thereof. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can inhibit a RNA dependent RNA polymerase. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can inhibit a HCV polymerase (for example, NS5B polymerase).

Some embodiments described herein relate to a method of treating HCV infection in a subject suffering from a HCV infection that can include administering to the subject an effective amount of a compound of Formula (I), or a pharmaceutical acceptable salt thereof, or a pharmaceutical composition that includes an effective amount of a compound of Formula (I), or a pharmaceutical acceptable salt thereof. Some embodiments described herein relate to a method of treating a condition selected from liver fibrosis, liver cirrhosis, and liver cancer in a subject suffering from one or more of the aforementioned liver conditions that can include administering to the subject an effective amount of a compound or a pharmaceutical composition described herein (for example, a compound of Formula (I), or a pharmaceutical acceptable salt thereof). One cause of liver fibrosis, liver cirrohis, and/or liver cancer can be a HCV infection. Some embodiments described herein relate to a method of increasing liver function in a subject having a HCV infection that can include administering to the subject an effective amount of a compound or a pharmaceutical composition described herein (for example, a compound of Formula (I), or a pharmaceutical acceptable salt thereof). Also contemplated is a method for reducing or eliminating further virus-caused liver damage in a subject having an HCV infection by administering to the subject an effective amount of a compound or a pharmaceutical composition described herein (for example, a compound of Formula (I), or a pharmaceutical acceptable salt thereof). In some embodiments, this method can include slowing or halting the progression of liver disease. In other embodiments, the course of the disease can be reversed, and stasis or improvement in liver function is contemplated.

There are a variety of genotypes of HCV, and a variety of subtypes within each genotype. For example, at present it is known that there are eleven (numbered 1 through 11) main genotypes of HCV, although others have classified the genotypes as 6 main genotypes. Each of these genotypes is further subdivided into subtypes (1a-1c; 2a-2c; 3a-3b; 4a-4e; 5a; 6a; 7a-7b; 8a-8b; 9a; 10a; and 11a). In some embodiments, an effective amount of a compound of Formula (I), or a pharmaceutical acceptable salt thereof, or a pharmaceutical composition that includes an effective amount of a compound of Formula (I), or a pharmaceutical acceptable salt thereof, can be effective to treat at least one genotype of HCV. In some embodiments, a compound described herein (for example, a compound of Formula (I), or a pharmaceutical acceptable salt thereof) can be effective to treat all 11 genotypes of HCV. In some embodiments, a compound described herein (for example, a compound of Formula (I), or a pharmaceutical acceptable salt thereof) can be effective to treat 3 or more, 5 or more, 7 or more, or 9 or more genotypes of HCV. In some embodiments, a compound of Formula (I), or a pharmaceutical acceptable salt thereof can be more effective against a larger number of HCV genotypes than the standard of care. In some embodiments, a compound of Formula (I), or a pharmaceutical acceptable salt thereof, can be more effective against a particular HCV genotype than the standard of care (such as genotype 1, 2, 3, 4, 5 and/or 6).

Various indicators for determining the effectiveness of a method for treating a HCV infection are known to those skilled in the art. Examples of suitable indicators include, but are not limited to, a reduction in viral load, a reduction in viral replication, a reduction in time to seroconversion (virus undetectable in patient serum), an increase in the rate of sustained viral response to therapy, a reduction of morbidity or mortality in clinical outcomes, a reduction in the rate of liver function decrease; stasis in liver function; improvement in liver function; reduction in one or more markers of liver dysfunction, including alanine transaminase, aspartate transaminase, total bilirubin, conjugated bilirubin, gamma glutamyl transpeptidase, and/or other indicator of disease response. Similarly, successful therapy with an effective amount of a compound or a pharmaceutical composition described herein (for example, a compound of Formula (I), or a pharmaceutical acceptable salt thereof) can reduce the incidence of liver cancer in HCV infected subjects.

In some embodiments, an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, is an amount that is effective to reduce viral titers to undetectable levels, for example, to about 100 to about 500, to about 50 to about 100, to about 10 to about 50, or to about 15 to about 25 international units/mL serum. In some embodiments, an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, is an amount that is effective to reduce viral load compared to the viral load before administration of the compound of Formula (I), or a pharmaceutically acceptable salt thereof. For example, wherein the viral load is measured before administration of the compound of Formula (I), or a pharmaceutically acceptable salt thereof, and again after completion of the treatment regime with the compound of Formula (I), or a pharmaceutically acceptable salt thereof (for example, 1 month after completion). In some embodiments, an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be an amount that is effective to reduce viral load to lower than about 25 international units/mL serum. In some embodiments, an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, is an amount that is effective to achieve a reduction in viral titer in the serum of the subject in the range of about 1.5-log to about a 2.5-log reduction, about a 3-log to about a 4-log reduction, or a greater than about 5-log reduction compared to the viral load before administration of the compound of Formula (I), or a pharmaceutically acceptable salt thereof. For example, the viral load can be measured before administration of the compound of Formula (I), or a pharmaceutically acceptable salt thereof, and again after completion of the treatment regime with the compound of Formula (I), or a pharmaceutically acceptable salt thereof (for example, 1 month after completion).

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can result in at least a 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, 75, 100-fold or more reduction in the replication of HCV relative to pre-treatment levels in a subject, as determined after completion of the treatment regime (for example 1 month after completion). In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can result in a reduction of the replication of HCV relative to pre-treatment levels in the range of about 2 to about 5 fold, about 10 to about 20 fold, about 15 to about 40 fold, or about 50 to about 100 fold. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can result in a reduction of HCV replication in the range of 1 to 1.5 log, 1.5 log to 2 log, 2 log to 2.5 log, 2.5 to 3 log, 3 log to 3.5 log or 3.5 to 4 log more reduction of HCV replication compared to the reduction of HCV reduction achieved by pegylated interferon in combination with ribavirin, administered according to the standard of care, or may achieve the same reduction as that standard of care therapy in a shorter period of time, for example, in one month, two months, or three months, as compared to the reduction achieved after six months of standard of care therapy with ribavirin and pegylated interferon.

In some embodiments, an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, is an amount that is effective to achieve a sustained viral response, for example, non-detectable or substantially non-detectable HCV RNA (e.g., less than about 500, less than about 400, less than about 200, or less than about 100 genome copies per milliliter serum) is found in the subject's serum for a period of at least about one month, at least about two months, at least about three months, at least about four months, at least about five months, or at least about six months following cessation of therapy.

In some embodiments, a therapeutically effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can reduce a level of a marker of liver fibrosis by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, or at least about 80%, or more, compared to the level of the marker in an untreated subject, or to a placebo-treated subject. Methods of measuring serum markers are known to those skilled in the art and include immunological-based methods, e.g., enzyme-linked immunosorbent assays (ELISA), radioimmunoassays, and the like, using antibody specific for a given serum marker. A non-limiting list of examples of a markers includes measuring the levels of serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), gamma-glutamyl transpeptidase (GGT) and total bilirubin (TBIL) using known methods. In general, an ALT level of less than about 45 IU/L (international units/liter), an AST in the range of 10-34 IU/L, ALP in the range of 44-147 IU/L, GGT in the range of 0-51 IU/L, TBIL in the range of 0.3-1.9 mg/dL is considered normal. In some embodiments, an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be an amount effective to reduce ALT, AST, ALP, GGT and/or TBIL levels to with what is considered a normal level.

Subjects who are clinically diagnosed with HCV infection include “naïve” subjects (e.g., subjects not previously treated for HCV, particularly those who have not previously received IFN-alpha-based and/or ribavirin-based therapy) and individuals who have failed prior treatment for HCV (“treatment failure” subjects). Treatment failure subjects include “non-responders” (i.e., subjects in whom the HCV titer was not significantly or sufficiently reduced by a previous treatment for HCV (≦0.5 log IU/mL), for example, a previous IFN-alpha monotherapy, a previous IFN-alpha and ribavirin combination therapy, or a previous pegylated IFN-alpha and ribavirin combination therapy); and “relapsers” (i.e., subjects who were previously treated for HCV, for example, who received a previous IFN-alpha monotherapy, a previous IFN-alpha and ribavirin combination therapy, or a previous pegylated IFN-alpha and ribavirin combination therapy, whose HCV titer decreased, and subsequently increased).

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a treatment failure subject suffering from HCV. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a non-responder subject suffering from HCV. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a relapsed subject suffering from HCV.

After a period of time, infectious agents can develop resistance to one or more therapeutic agents. The term “resistance” as used herein refers to a viral strain displaying a delayed, lessened and/or null response to a therapeutic agent(s). For example, after treatment with an antiviral agent, the viral load of a subject infected with a resistant virus may be reduced to a lesser degree compared to the amount in viral load reduction exhibited by a subject infected with a non-resistant strain. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a subject infected with an HCV strain that is resistant to one or more different anti-HCV agents. In some embodiments, development of resistant HCV strains is delayed when a subject is treated with a compound of Formula (I), or a pharmaceutically acceptable salt thereof, compared to the development of HCV strains resistant to other HCV drugs.

In some embodiments, an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a subject for whom other anti-HCV medications are contraindicated. For example, administration of pegylated interferon alpha in combination with ribavirin is contraindicated in subjects with hemoglobinopathies (e.g., thalassemia major, sickle-cell anemia) and other subjects at risk from the hematologic side effects of current therapy. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be provided to a subject that is hypersensitive to interferon and/or ribavirin.

Some subjects being treated for HCV experience a viral load rebound. The term “viral load rebound” as used herein refers to a sustained ≧0.5 log IU/mL increase of viral load above nadir before the end of treatment, where nadir is a ≧0.5 log IU/mL decrease from baseline. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a subject experiencing viral load rebound, or can prevent such viral load rebound when used to treat the subject.

The standard of care for treating HCV has been associated with several side effects (adverse events). In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can decrease the number and/or severity of side effects that can be observed in HCV patients being treated with ribavirin and pegylated interferon according to the standard of care. Examples of side effects include, but are not limited to fever, malaise, tachycardia, chills, headache, arthralgias, myalgias, fatigue, apathy, loss of appetite, nausea, vomiting, cognitive changes, asthenia, drowsiness, lack of initiative, irritability, confusion, depression, severe depression, suicidal ideation, anemia, low white blood cell counts, and thinning of hair. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be provided to a subject that discontinued a HCV therapy because of one or more adverse effects or side effects associated with one or more other HCV agents.

Table 1 provides some embodiments of the percentage improvement obtained using a compound of Formula (I), or a pharmaceutically acceptable salt thereof, as compared to the standard of care. Examples include the following: in some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, results in a percentage of non-responders that is 10% less than the percentage of non-responders receiving the standard of care; in some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, results in a number of side effects that is in the range of about 10% to about 30% less than compared to the number of side effects experienced by a subject receiving the standard of care; and in some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, results in a severity of a side effect (such as one of those described herein) that is 25% less than compared to the severity of the same side effect experienced by a subject receiving the standard of care. Methods of quantifying the severity of a side effect are known to those skilled in the art.

TABLE 1 Percentage Percentage of of Percentage Percent viral Number Severity non- of of load of side of side responders relapsers resistance rebound effects effects 10% less 10% less 10% less 10% less 10% less 10% less 25% less 25% less 25% less 25% less 25% less 25% less 40% less 40% less 40% less 40% less 40% less 40% less 50% less 50% less 50% less 50% less 50% less 50% less 60% less 60% less 60% less 60% less 60% less 60% less 70% less 70% less 70% less 70% less 70% less 70% less 80% less 80% less 80% less 80% less 80% less 80% less 90% less 90% less 90% less 90% less 90% less 90% less about 10% about 10% about 10% about 10% about 10% about 10% to about to about to about to about to about to about 30% less 30% less 30% less 30% less 30% less 30% less about 20% about 20% about 20% about 20% about 20% about 20% to about to about to about to about to about to about 50% less 50% less 50% less 50% less 50% less 50% less about 30% about 30% about 30% about 30% about 30% about 30% to about to about to about to about to about to about 70% less 70% less 70% less 70% less 70% less 70% less about 20% about 20% about 20% about 20% about 20% about 20% to about to about to about to about to about to about 80% less 80% less 80% less 80% less 80% less 80% less

Yet still other embodiments disclosed herein relates to a method of ameliorating or treating a parasitic disease that can include administering to a subject suffering from a parasitic disease a therapeutically effective amount of one or more compounds described herein (for example, a compound of Formula (I)), or a pharmaceutical composition that includes one or more compounds described herein. In some embodiments, the parasite disease can be Chagas' disease.

As used herein, a “subject” refers to an animal that is the object of treatment, observation or experiment. “Animal” includes cold- and warm-blooded vertebrates and invertebrates such as fish, shellfish, reptiles and, in particular, mammals. “Mammal” includes, without limitation, mice, rats, rabbits, guinea pigs, dogs, cats, sheep, goats, cows, horses, primates, such as monkeys, chimpanzees, and apes, and, in particular, humans. In some embodiments, the subject is human.

As used herein, the terms “treating,” “treatment,” “therapeutic,” or “therapy” do not necessarily mean total cure or abolition of the disease or condition. Any alleviation of any undesired signs or symptoms of a disease or condition, to any extent can be considered treatment and/or therapy. Furthermore, treatment may include acts that may worsen the patient's overall feeling of well-being or appearance.

The terms “therapeutically effective amount” and “effective amount” are used to indicate an amount of an active compound, or pharmaceutical agent, that elicits the biological or medicinal response indicated. For example, a therapeutically effective amount of compound can be the amount needed to prevent, alleviate or ameliorate symptoms of disease or prolong the survival of the subject being treated This response may occur in a tissue, system, animal or human and includes alleviation of the signs or symptoms of the disease being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art, in view of the disclosure provided herein. The therapeutically effective amount of the compounds disclosed herein required as a dose will depend on the route of administration, the type of animal, including human, being treated, and the physical characteristics of the specific animal under consideration. The dose can be tailored to achieve a desired effect, but will depend on such factors as weight, diet, concurrent medication and other factors which those skilled in the medical arts will recognize.

As will be readily apparent to one skilled in the art, the useful in vivo dosage to be administered and the particular mode of administration will vary depending upon the age, weight, the severity of the affliction, and mammalian species treated, the particular compounds employed, and the specific use for which these compounds are employed. The determination of effective dosage levels, that is the dosage levels necessary to achieve the desired result, can be accomplished by one skilled in the art using routine methods, for example, human clinical trials and in vitro studies.

The dosage may range broadly, depending upon the desired effects and the therapeutic indication. Alternatively dosages may be based and calculated upon the surface area of the patient, as understood by those of skill in the art. Although the exact dosage will be determined on a drug-by-drug basis, in most cases, some generalizations regarding the dosage can be made. The daily dosage regimen for an adult human patient may be, for example, an oral dose of between 0.01 mg and 3000 mg of each active ingredient, preferably between 1 mg and 700 mg, e.g. 5 to 200 mg. The dosage may be a single one or a series of two or more given in the course of one or more days, as is needed by the subject. In some embodiments, the compounds will be administered for a period of continuous therapy, for example for a week or more, or for months or years. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered less frequently compared to the frequency of administration of an agent within the standard of care. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered one time per day. For example, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered one time per day to a subject suffering from a HCV infection. In some embodiments, the total time of the treatment regime with a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can less compared to the total time of the treatment regime with the standard of care.

In instances where human dosages for compounds have been established for at least some condition, those same dosages may be used, or dosages that are between about 0.1% and 500%, more preferably between about 25% and 250% of the established human dosage. Where no human dosage is established, as will be the case for newly-discovered pharmaceutical compositions, a suitable human dosage can be inferred from ED₅₀ or ID₅₀ values, or other appropriate values derived from in vitro or in vivo studies, as qualified by toxicity studies and efficacy studies in animals.

In cases of administration of a pharmaceutically acceptable salt, dosages may be calculated as the free base. As will be understood by those of skill in the art, in certain situations it may be necessary to administer the compounds disclosed herein in amounts that exceed, or even far exceed, the above-stated, preferred dosage range in order to effectively and aggressively treat particularly aggressive diseases or infections.

Dosage amount and interval may be adjusted individually to provide plasma levels of the active moiety which are sufficient to maintain the modulating effects, or minimal effective concentration (MEC). The MEC will vary for each compound but can be estimated from in vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. However, HPLC assays or bioassays can be used to determine plasma concentrations. Dosage intervals can also be determined using MEC value. Compositions should be administered using a regimen which maintains plasma levels above the MEC for 10-90% of the time, preferably between 30-90% and most preferably between 50-90%. In cases of local administration or selective uptake, the effective local concentration of the drug may not be related to plasma concentration.

It should be noted that the attending physician would know how to and when to terminate, interrupt, or adjust administration due to toxicity or organ dysfunctions. Conversely, the attending physician would also know to adjust treatment to higher levels if the clinical response were not adequate (precluding toxicity). The magnitude of an administrated dose in the management of the disorder of interest will vary with the severity of the condition to be treated and to the route of administration. The severity of the condition may, for example, be evaluated, in part, by standard prognostic evaluation methods. Further, the dose and perhaps dose frequency, will also vary according to the age, body weight, and response of the individual patient. A program comparable to that discussed above may be used in veterinary medicine.

Compounds disclosed herein can be evaluated for efficacy and toxicity using known methods. For example, the toxicology of a particular compound, or of a subset of the compounds, sharing certain chemical moieties, may be established by determining in vitro toxicity towards a cell line, such as a mammalian, and preferably human, cell line. The results of such studies are often predictive of toxicity in animals, such as mammals, or more specifically, humans. Alternatively, the toxicity of particular compounds in an animal model, such as mice, rats, rabbits, or monkeys, may be determined using known methods. The efficacy of a particular compound may be established using several recognized methods, such as in vitro methods, animal models, or human clinical trials. When selecting a model to determine efficacy, the skilled artisan can be guided by the state of the art to choose an appropriate model, dose, route of administration and/or regime.

Combination Therapies

In some embodiments, the compounds disclosed herein, such as a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound described herein, or a pharmaceutically acceptable salt thereof, can be used in combination with one or more additional agent(s). Examples of additional agents that can be used in combination with a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, include, but are not limited to, agents currently used in a conventional standard of care for treating HCV, HCV protease inhibitors, HCV polymerase inhibitors, NS5A inhibitors, other antiviral compounds, pharmaceutically acceptable salts and pharmaceutical compositions that can include compounds of Formula (BB) (including pharmaceutically acceptable salts and pharmaceutical compositions that can include a compound of Formula (BB), or a pharmaceutically acceptable salt thereof), compounds of Formula (CC) (including pharmaceutically acceptable salts and pharmaceutical compositions that can include a compound of Formula (CC), or a pharmaceutically acceptable salt thereof), and/or combinations thereof. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used with one, two, three or more additional agents described herein. A non-limiting list of examples of combinations of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, is provided in Tables A, B, C and D.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with an agent(s) currently used in a conventional standard of care therapy. For example, for the treatment of HCV, a compound disclosed herein can be used in combination with Pegylated interferon-alpha-2a (brand name PEGASYS®) and ribavirin, or Pegylated interferon-alpha-2b (brand name PEG-INTRON®) and ribavirin. As another example, a compound disclosed herein can be used in combination with oseltamivir (TAMIFLU®) or zanamivin (RELENZA®) for treating an influenza infection.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be substituted for an agent currently used in a conventional standard of care therapy. For example, for the treatment of HCV, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in place of ribavirin.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with an interferon, such as a pegylated interferon. Examples of suitable interferons include, but are not limited to, Pegylated interferon-alpha-2a (brand name PEGASYS®), Pegylated interferon-alpha-2b (brand name PEG-INTRON®), interferon alfacon-1 (brand name INFERGEN®), pegylated interferon lambda and/or a combination thereof

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a HCV protease inhibitor. A non-limiting list of example HCV protease inhibitors include the following: VX-950 (TELAPREVIR®), MK-5172, ABT-450, BILN-2061, BI-201335, BMS-650032, SCH 503034 (BOCEPREVIR®), GS-9256, GS-9451, IDX-320, ACH-1625, ACH-2684, TMC-435, ITMN-191 (DANOPREVIR®) and/or a combination thereof. Additional HCV protease inhibitors suitable for use in combination with a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, include VP-19744, PSI-879, VCH-759/VX-759, HCV-371, IDX-375, GL-60667, JTK-109, PSI-6130, R1479, R-1626, R-7182, MK-0608, INX-8014, INX-8018, A-848837, A-837093, BILB-1941, VCH-916, VCH-716, GSK-71185, GSK-625433, XTL-2125 and those disclosed in PCT Publication No. WO 2012/142085. A non-limiting list of example HCV protease inhibitors includes the compounds numbered 1001-1016 in FIG. 1.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a HCV polymerase inhibitor. In some embodiments, the HCV polymerase inhibitor can be a nucleoside inhibitor. In other embodiments, the HCV polymerase inhibitor can be a non-nucleoside inhibitor. Examples of suitable nucleoside inhibitors include, but are not limited to, RG7128, PSI-7851, PSI-7977, INX-189, PSI-352938, PSI-661, 4′-azidouridine (including known prodrugs of 4′-azidouridine), GS-6620, IDX-184, and TMC649128 and/or combinations thereof. A non-limiting list of example nucleoside inhibitors includes compounds numbered 2001-2012 in FIG. 2. Examples of suitable non-nucleoside inhibitors include, but are not limited to, ABT-333, ANA-598, VX-222, HCV-796, BI-207127, GS-9190, PF-00868554 (FILIBUVIR®), VX-497 and/or combinations thereof. A non-limiting list of example non-nucleoside inhibitors includes the compounds numbered 3001-3014 in FIG. 3. Further HCV polymerase inhibitors suitable for use in combination with a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, include VX-500, VX-813, VBY-376, TMC-435350, EZ-058, EZ-063, GS-9132, ACH-1095, IDX-136, IDX-316, ITMN-8356, ITMN-8347, ITMN-8096, ITMN-7587, VX-985, and those disclosed in PCT Publication No. WO 2012/142085.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a NS5A inhibitor. A non-limiting list of example NS5A inhibitors include BMS-790052, PPI-461, ACH-2928, GS-5885, BMS-824393 and/or combinations thereof. A non-limiting list of example NS5A inhibitors includes the compounds numbered 4001-4012 in FIG. 4. Additional NS5A inhibitors suitable for use in combination with a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, include A-832, PPI-1301 and those disclosed in PCT Publication No. WO 2012/142085, which is hereby incorporated by reference for the limited purpose of its disclosure of HCV protease inhibitors, HCV polymerase inhibitors and NS5A inhibitors.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with other antiviral compounds. Examples of other antiviral compounds include, but are not limited to, Debio-025, MIR-122 and/or combinations thereof. A non-limiting list of example other antiviral compounds includes the compounds numbered 5001-5011 in FIG. 5.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a compound of Formula (BB), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (BB), or a pharmaceutically acceptable salt thereof (see, U.S. Publication No. 2012/0165286, published Jun. 28, 2012, the contents of which are incorporated by reference in their entireties):

wherein B^(BB1) can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group; X^(BB) can be O (oxygen) or S (sulfur); R^(BB1) can be selected from —Z^(BB)—R^(BB9), an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; Z^(BB) can be selected from O (oxygen), S (sulfur) and N(R^(BB10)); R^(BB2) and R^(BB3) can be independently selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl, an optionally substituted C₁₋₆ haloalkyl and an optionally substituted aryl(C₁₋₆ alkyl); or R^(BB2) and R^(BB3) can be taken together to form a group selected from an optionally substituted C₃₋₆ cycloalkyl, an optionally substituted C₃₋₆ cycloalkenyl, an optionally substituted C₃₋₆ aryl and an optionally substituted C₃₋₆ heteroaryl; R^(BB4) can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl and an optionally substituted allenyl; R^(BB5) can be hydrogen or an optionally substituted C₁₋₆ alkyl; R^(BB6) can be selected from hydrogen, halogen, azido, amino, cyano, an optionally substituted C₁₋₆ alkyl, —OR^(BB11) and —OC(═O)R^(BB12); R^(BB7) can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR^(BB13) and —OC(═O)R^(BB14); R^(BB8) can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR^(BB15) and —OC(═O)R^(BB16); R^(BB9) can be selected from an optionally substituted alkyl, an optionally substituted alkenyl, an optionally substituted alkynyl, an optionally substituted cycloalkyl, an optionally substituted cycloalkenyl, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl, an optionally substituted aryl(C₁₋₆ alkyl), an optionally substituted heteroaryl(C₁₋₆ alkyl) and an optionally substituted heterocyclyl(C₁₋₆ alkyl); R^(BB10) can be selected from hydrogen, an optionally substituted alkyl, an optionally substituted alkenyl, an optionally substituted alkynyl, an optionally substituted cycloalkyl, an optionally substituted cycloalkenyl, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl, an optionally substituted aryl(C₁₋₆ alkyl), an optionally substituted heteroaryl(C₁₋₆ alkyl) and an optionally substituted heterocyclyl(C₁₋₆ alkyl); R^(BB11), R^(BB13) and R^(BB15) can be independently hydrogen or an optionally substituted C₁₋₆ alkyl; and R^(BB12), R^(BB14) and R^(BB16) can be independently an optionally substituted C₁₋₆ alkyl or an optionally substituted C₃₋₆ cycloalkyl. In some embodiments, at least one of R^(BB2) and R^(BB3) is not hydrogen. A non-limiting list of example compounds of Formula (BB) includes the compound numbered 7000-7016 in FIG. 7.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a compound of Formula (CC), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (CC), or a pharmaceutically acceptable salt thereof (see, U.S. Publication No. 2012/0071434, published Mar. 22, 2012, the contents of which are incorporated by reference in its entirety):

wherein B^(CC1) can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group; R^(CC1) can be selected from O⁻, OH, an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; R^(CC2) can be selected from an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl and

wherein R^(CC19), R^(CC20) and R^(CC21) can be independently absent or hydrogen, and n^(CC) can be 0 or 1; provided that when R^(CC1) is O⁻ or OH, then R^(CC2) is

R^(CC3a) and R^(CC3b) can be independently selected from hydrogen, deuterium, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl, an optionally substituted C₁₋₆ haloalkyl and aryl(C₁₋₆ alkyl); or R^(CC3a) and R^(CC3b) can be taken together to form an optionally substituted C₃₋₆ cycloalkyl; R^(CC4) can be selected from hydrogen, azido, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl and an optionally substituted C₂₋₆ alkynyl; R^(CC5) can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR^(CC10) and —OC(═O)R^(CC11); R^(CC6) can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR^(CC12) and —OC(═O)R^(CC13); R^(CC7) can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR^(CC14) and —OC(═O)R^(CC15); or R^(CC6) and R^(CC7) can be both oxygen atoms and linked together by a carbonyl group; R^(CC8) can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR^(CC16) and —OC(═O)R^(CC17); R^(CC9) can be selected from hydrogen, azido, cyano, an optionally substituted C₁₋₆ alkyl and —OR^(CC18); R^(CC10), R^(CC12), R^(CC14), R^(CC16) and R^(CC18) can be independently selected from hydrogen and an optionally substituted C₁₋₆ alkyl; and R^(CC11), R^(CC13), R^(CC15) and R^(CC17) can be independently selected from an optionally substituted C₁₋₆ alkyl and an optionally substituted C₃₋₆ cycloalkyl. In some embodiments, when R^(CC3a), R^(CC3b), R^(CC4), R^(CC5), R^(CC7), R^(CC8) and R^(CC9) are all hydrogen, then R^(CC6) is not azido. In some embodiments, R^(CC2) cannot be

when R^(CC3a) is hydrogen, R^(CC3b) is hydrogen, R^(CC4) is H, R^(CC5) is OH or H, R^(CC6) is hydrogen, OH, or —OC(═O)CH₃, R^(CC7) is hydrogen, OH, OCH₃ or —OC(═O)CH₃, R^(CC8) is hydrogen, OH or OCH₃, R^(CC9) is H and B^(CC1) is an optionally substituted adenine, an optionally substituted guanine, an optionally substituted uracil or an optionally substituted hypoxanthine. In some embodiments, R^(CC2) cannot be

A non-limiting list of examples of compounds of Formula (CC) includes the compounds numbered 6000-6078 in FIG. 6.

Some embodiments described herein relate to a method of ameliorating or treating a viral infection that can include contacting a cell infected with the viral infection with a therapeutically effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (BB) and a compound of Formula (CC), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

Some embodiments described herein relate to a method of ameliorating or treating a viral infection that can include administering to a subject suffering from the viral infection a therapeutically effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (BB) and a compound of Formula (CC), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

Some embodiments described herein relate to a method of inhibiting viral replication of a virus that can include contacting a cell infected with the virus with an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (BB) and a compound of Formula (CC), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

Some embodiments described herein relate to a method of ameliorating or treating a viral infection that can include contacting a cell infected with the viral infection with a therapeutically effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (BB) and a compound of Formula (CC), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

Some embodiments described herein relate to a method of ameliorating or treating a viral infection that can include administering to a subject suffering from the viral infection a therapeutically effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (BB) and a compound of Formula (CC), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

Some embodiments described herein relate to a method of inhibiting viral replication of a virus that can include contacting a cell infected with the virus with an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (BB) and a compound of Formula (CC), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered with one or more additional agent(s) together in a single pharmaceutical composition. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt the thereof, can be administered with one or more additional agent(s) as two or more separate pharmaceutical compositions. For example, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered in one pharmaceutical composition, and at least one of the additional agents can be administered in a second pharmaceutical composition. If there are at least two additional agents, one or more of the additional agents can be in a first pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and at least one of the other additional agent(s) can be in a second pharmaceutical composition.

The dosing amount(s) and dosing schedule(s) when using a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and one or more additional agents are within the knowledge of those skilled in the art. For example, when performing a conventional standard of care therapy using art-recognized dosing amounts and dosing schedules, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered in addition to that therapy, or in place of one of the agents of a combination therapy, using effective amounts and dosing protocols as described herein.

The order of administration of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, with one or more additional agent(s) can vary. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered prior to all additional agents. In other embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered prior to at least one additional agent. In still other embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered concomitantly with one or more additional agent(s). In yet still other embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered subsequent to the administration of at least one additional agent. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered subsequent to the administration of all additional agents.

In some embodiments, the combination of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof) can result in an additive effect. In some embodiments, the combination of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof) can result in a synergistic effect. In some embodiments, the combination of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof) can result in a strongly synergistic effect. In some embodiments, the combination of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof) is not antagonistic.

As used herein, the term “antagonistic” means that the activity of the combination of compounds is less compared to the sum of the activities of the compounds in combination when the activity of each compound is determined individually (i.e. as a single compound). As used herein, the term “synergistic effect” means that the activity of the combination of compounds is greater than the sum of the individual activities of the compounds in the combination when the activity of each compound is determined individually. As used herein, the term “additive effect” means that the activity of the combination of compounds is about equal to the sum of the individual activities of the compound in the combination when the activity of each compound is determined individually.

A potential advantage of utilizing a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof) may be a reduction in the required amount(s) of one or more compounds of FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof) that is effective in treating a disease condition disclosed herein (for example, HCV), as compared to the amount required to achieve same therapeutic result when one or more compounds of FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof) are administered without a compound of Formula (I), or a pharmaceutically acceptable salt thereof. For example, the amount of a compound in FIGS. 1-7 (including a pharmaceutically acceptable salt and prodrug thereof), can be less compared to the amount of the compound in FIGS. 1-7 (including a pharmaceutically acceptable salt and prodrug thereof), needed to achieve the same viral load reduction when administered as a monotherapy. Another potential advantage of utilizing a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof) is that the use of two or more compounds having different mechanism of actions can create a higher barrier to the development of resistant viral strains compared to the barrier when a compound is administered as monotherapy.

Additional advantages of utilizing a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof) may include little to no cross resistance between a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof) thereof; different routes for elimination of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof); little to no overlapping toxicities between a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof); little to no significant effects on cytochrome P450; and/or little to no pharmacokinetic interactions between a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and one or more additional agent(s) in FIGS. 1-7 (including pharmaceutically acceptable salts and prodrugs thereof).

A non-limiting list of example combination of compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound described herein, with one or more additional agent(s) are provided in Tables A, B, C and D. Each numbered X and Y compound in Tables A, B, C and D has a corresponding name and/or structure provided in FIGS. 1-7. The numbered compounds in Tables A, B, C and D includes pharmaceutically acceptable salts of the compounds and pharmaceutical compositions containing the compounds or a pharmaceutically acceptable salt thereof. For example, 1001 includes the compound corresponding to 1001, pharmaceutically acceptable salts thereof, and pharmaceutical compositions that include compound 1001 and/or a pharmaceutically acceptable salt thereof. The combinations exemplified in Tables A, B, C and D are designated by the formula X:Y, which represents a combination of a compound X with a compound Y. For example, the combination designated as 1001:8001 in Table A represents a combination of compound 1001 with compound 8001, including pharmaceutically acceptable salts of compound 1001 and/or 8001, and pharmaceutical compositions including compound 1001 and 8001 (including pharmaceutical compositions that include pharmaceutically acceptable salts of compound 1001 and/or compound 8001). Thus, the combination designated as 1001:8001 in Table A represents the combination of Telaprevir (compound 1001, as shown in FIG. 1) and

(compound 8001, as shown in FIG. 8), including pharmaceutically acceptable salts of compound 1001 and/or 8001, and pharmaceutical compositions including compound 1001 and 8001 (including pharmaceutical compositions that include pharmaceutically acceptable salts of compound 1001 and/or compound 8001). Each of the combinations provided in Tables A, B, C and D can be used with one, two, three or more additional agents described herein. In some embodiments described herein, the combination of agents can be used to treat, ameliorate and/or inhibit a virus and/or a viral infection, wherein the virus can be HCV and the viral infection can be an HCV viral infection.

TABLE A Example combinations of a compound X with a compound Y. X:Y X:Y X:Y X:Y X:Y X:Y 1001:8000 1001:8001 1001:8002 1001:8003 1001:8004 1001:8005 1002:8000 1002:8001 1002:8002 1002:8003 1002:8004 1002:8005 1003:8000 1003:8001 1003:8002 1003:8003 1003:8004 1003:8005 1004:8000 1004:8001 1004:8002 1004:8003 1004:8004 1004:8005 1005:8000 1005:8001 1005:8002 1005:8003 1005:8004 1005:8005 1006:8000 1006:8001 1006:8002 1006:8003 1006:8004 1006:8005 1007:8000 1007:8001 1007:8002 1007:8003 1007:8004 1007:8005 1008:8000 1008:8001 1008:8002 1008:8003 1008:8004 1008:8005 1009:8000 1009:8001 1009:8002 1009:8003 1009:8004 1009:8005 1010:8000 1010:8001 1010:8002 1010:8003 1010:8004 1010:8005 1011:8000 1011:8001 1011:8002 1011:8003 1011:8004 1011:8005 1012:8000 1012:8001 1012:8002 1012:8003 1012:8004 1012:8005 1013:8000 1013:8001 1013:8002 1013:8003 1013:8004 1013:8005 1014:8000 1014:8001 1014:8002 1014:8003 1014:8004 1014:8005 1015:8000 1015:8001 1015:8002 1015:8003 1015:8004 1015:8005 1016:8000 1016:8001 1016:8002 1016:8003 1016:8004 1016:8005 2001:8000 2001:8001 2001:8002 2001:8003 2001:8004 2001:8005 2002:8000 2002:8001 2002:8002 2002:8003 2002:8004 2002:8005 2003:8000 2003:8001 2003:8002 2003:8003 2003:8004 2003:8005 2004:8000 2004:8001 2004:8002 2004:8003 2004:8004 2004:8005 2005:8000 2005:8001 2005:8002 2005:8003 2005:8004 2005:8005 2006:8000 2006:8001 2006:8002 2006:8003 2006:8004 2006:8005 2007:8000 2007:8001 2007:8002 2007:8003 2007:8004 2007:8005 2008:8000 2008:8001 2008:8002 2008:8003 2008:8004 2008:8005 2009:8000 2009:8001 2009:8002 2009:8003 2009:8004 2009:8005 2010:8000 2010:8001 2010:8002 2010:8003 2010:8004 2010:8005 2011:8000 2011:8001 2011:8002 2011:8003 2011:8004 2011:8005 2012:8000 2012:8001 2012:8002 2012:8003 2012:8004 2012:8005 3001:8000 3001:8001 3001:8002 3001:8003 3001:8004 3001:8005 3002:8000 3002:8001 3002:8002 3002:8003 3002:8004 3002:8005 3003:8000 3003:8001 3003:8002 3003:8003 3003:8004 3003:8005 3004:8000 3004:8001 3004:8002 3004:8003 3004:8004 3004:8005 3005:8000 3005:8001 3005:8002 3005:8003 3005:8004 3005:8005 3006:8000 3006:8001 3006:8002 3006:8003 3006:8004 3006:8005 3007:8000 3007:8001 3007:8002 3007:8003 3007:8004 3007:8005 3008:8000 3008:8001 3008:8002 3008:8003 3008:8004 3008:8005 3009:8000 3009:8001 3009:8002 3009:8003 3009:8004 3009:8005 3010:8000 3010:8001 3010:8002 3010:8003 3010:8004 3010:8005 3011:8000 3011:8001 3011:8002 3011:8003 3011:8004 3011:8005 3012:8000 3012:8001 3012:8002 3012:8003 3012:8004 3012:8005 3013:8000 3013:8001 3013:8002 3013:8003 3013:8004 3013:8005 3014:8000 3014:8001 3014:8002 3014:8003 3014:8004 3014:8005 1001:8006 1001:8007 1001:8008 1001:8009 1001:8010 1001:8011 1002:8006 1002:8007 1002:8008 1002:8009 1002:8010 1002:8011 1003:8006 1003:8007 1003:8008 1003:8009 1003:8010 1003:8011 1004:8006 1004:8007 1004:8008 1004:8009 1004:8010 1004:8011 1005:8006 1005:8007 1005:8008 1005:8009 1005:8010 1005:8011 1006:8006 1006:8007 1006:8008 1006:8009 1006:8010 1006:8011 1007:8006 1007:8007 1007:8008 1007:8009 1007:8010 1007:8011 1008:8006 1008:8007 1008:8008 1008:8009 1008:8010 1008:8011 1009:8006 1009:8007 1009:8008 1009:8009 1009:8010 1009:8011 1010:8006 1010:8007 1010:8008 1010:8009 1010:8010 1010:8011 1011:8006 1011:8007 1011:8008 1011:8009 1011:8010 1011:8011 1012:8006 1012:8007 1012:8008 1012:8009 1012:8010 1012:8011 1013:8006 1013:8007 1013:8008 1013:8009 1013:8010 1013:8011 1014:8006 1014:8007 1014:8008 1014:8009 1014:8010 1014:8011 1015:8006 1015:8007 1015:8008 1015:8009 1015:8010 1015:8011 1016:8006 1016:8007 1016:8008 1016:8009 1016:8010 1016:8011 2001:8006 2001:8007 2001:8008 2001:8009 2001:8010 2001:8011 2002:8006 2002:8007 2002:8008 2002:8009 2002:8010 2002:8011 2003:8006 2003:8007 2003:8008 2003:8009 2003:8010 2003:8011 2004:8006 2004:8007 2004:8008 2004:8009 2004:8010 2004:8011 2005:8006 2005:8007 2005:8008 2005:8009 2005:8010 2005:8011 2006:8006 2006:8007 2006:8008 2006:8009 2006:8010 2006:8011 2007:8006 2007:8007 2007:8008 2007:8009 2007:8010 2007:8011 2008:8006 2008:8007 2008:8008 2008:8009 2008:8010 2008:8011 2009:8006 2009:8007 2009:8008 2009:8009 2009:8010 2009:8011 2010:8006 2010:8007 2010:8008 2010:8009 2010:8010 2010:8011 2011:8006 2011:8007 2011:8008 2011:8009 2011:8010 2011:8011 2012:8006 2012:8007 2012:8008 2012:8009 2012:8010 2012:8011 3001:8006 3001:8007 3001:8008 3001:8009 3001:8010 3001:8011 3002:8006 3002:8007 3002:8008 3002:8009 3002:8010 3002:8011 3003:8006 3003:8007 3003:8008 3003:8009 3003:8010 3003:8011 3004:8006 3004:8007 3004:8008 3004:8009 3004:8010 3004:8011 3005:8006 3005:8007 3005:8008 3005:8009 3005:8010 3005:8011 3006:8006 3006:8007 3006:8008 3006:8009 3006:8010 3006:8011 3007:8006 3007:8007 3007:8008 3007:8009 3007:8010 3007:8011 3008:8006 3008:8007 3008:8008 3008:8009 3008:8010 3008:8011 3009:8006 3009:8007 3009:8008 3009:8009 3009:8010 3009:8011 3010:8006 3010:8007 3010:8008 3010:8009 3010:8010 3010:8011 3011:8006 3011:8007 3011:8008 3011:8009 3011:8010 3011:8011 3012:8006 3012:8007 3012:8008 3012:8009 3012:8010 3012:8011 3013:8006 3013:8007 3013:8008 3013:8009 3013:8010 3013:8011 3014:8006 3014:8007 3014:8008 3014:8009 3014:8010 3014:8011 1001:8012 1001:8013 1001:8014 1001:8015 1001:8016 1001:8017 1002:8012 1002:8013 1002:8014 1002:8015 1002:8016 1002:8017 1003:8012 1003:8013 1003:8014 1003:8015 1003:8016 1003:8017 1004:8012 1004:8013 1004:8014 1004:8015 1004:8016 1004:8017 1005:8012 1005:8013 1005:8014 1005:8015 1005:8016 1005:8017 1006:8012 1006:8013 1006:8014 1006:8015 1006:8016 1006:8017 1007:8012 1007:8013 1007:8014 1007:8015 1007:8016 1007:8017 1008:8012 1008:8013 1008:8014 1008:8015 1008:8016 1008:8017 1009:8012 1009:8013 1009:8014 1009:8015 1009:8016 1009:8017 1010:8012 1010:8013 1010:8014 1010:8015 1010:8016 1010:8017 1011:8012 1011:8013 1011:8014 1011:8015 1011:8016 1011:8017 1012:8012 1012:8013 1012:8014 1012:8015 1012:8016 1012:8017 1013:8012 1013:8013 1013:8014 1013:8015 1013:8016 1013:8017 1014:8012 1014:8013 1014:8014 1014:8015 1014:8016 1014:8017 1015:8012 1015:8013 1015:8014 1015:8015 1015:8016 1015:8017 1016:8012 1016:8013 1016:8014 1016:8015 1016:8016 1016:8017 2001:8012 2001:8013 2001:8014 2001:8015 2001:8016 2001:8017 2002:8012 2002:8013 2002:8014 2002:8015 2002:8016 2002:8017 2003:8012 2003:8013 2003:8014 2003:8015 2003:8016 2003:8017 2004:8012 2004:8013 2004:8014 2004:8015 2004:8016 2004:8017 2005:8012 2005:8013 2005:8014 2005:8015 2005:8016 2005:8017 2006:8012 2006:8013 2006:8014 2006:8015 2006:8016 2006:8017 2007:8012 2007:8013 2007:8014 2007:8015 2007:8016 2007:8017 2008:8012 2008:8013 2008:8014 2008:8015 2008:8016 2008:8017 2009:8012 2009:8013 2009:8014 2009:8015 2009:8016 2009:8017 2010:8012 2010:8013 2010:8014 2010:8015 2010:8016 2010:8017 2011:8012 2011:8013 2011:8014 2011:8015 2011:8016 2011:8017 2012:8012 2012:8013 2012:8014 2012:8015 2012:8016 2012:8017 3001:8012 3001:8013 3001:8014 3001:8015 3001:8016 3001:8017 3002:8012 3002:8013 3002:8014 3002:8015 3002:8016 3002:8017 3003:8012 3003:8013 3003:8014 3003:8015 3003:8016 3003:8017 3004:8012 3004:8013 3004:8014 3004:8015 3004:8016 3004:8017 3005:8012 3005:8013 3005:8014 3005:8015 3005:8016 3005:8017 3006:8012 3006:8013 3006:8014 3006:8015 3006:8016 3006:8017 3007:8012 3007:8013 3007:8014 3007:8015 3007:8016 3007:8017 3008:8012 3008:8013 3008:8014 3008:8015 3008:8016 3008:8017 3009:8012 3009:8013 3009:8014 3009:8015 3009:8016 3009:8017 3010:8012 3010:8013 3010:8014 3010:8015 3010:8016 3010:8017 3011:8012 3011:8013 3011:8014 3011:8015 3011:8016 3011:8017 3012:8012 3012:8013 3012:8014 3012:8015 3012:8016 3012:8017 3013:8012 3013:8013 3013:8014 3013:8015 3013:8016 3013:8017 3014:8012 3014:8013 3014:8014 3014:8015 3014:8016 3014:8017 1001:8018 1001:8019 1001:8020 1001:8021 1001:8022 1001:8023 1002:8018 1002:8019 1002:8020 1002:8021 1002:8022 1002:8023 1003:8018 1003:8019 1003:8020 1003:8021 1003:8022 1003:8023 1004:8018 1004:8019 1004:8020 1004:8021 1004:8022 1004:8023 1005:8018 1005:8019 1005:8020 1005:8021 1005:8022 1005:8023 1006:8018 1006:8019 1006:8020 1006:8021 1006:8022 1006:8023 1007:8018 1007:8019 1007:8020 1007:8021 1007:8022 1007:8023 1008:8018 1008:8019 1008:8020 1008:8021 1008:8022 1008:8023 1009:8018 1009:8019 1009:8020 1009:8021 1009:8022 1009:8023 1010:8018 1010:8019 1010:8020 1010:8021 1010:8022 1010:8023 1011:8018 1011:8019 1011:8020 1011:8021 1011:8022 1011:8023 1012:8018 1012:8019 1012:8020 1012:8021 1012:8022 1012:8023 1013:8018 1013:8019 1013:8020 1013:8021 1013:8022 1013:8023 1014:8018 1014:8019 1014:8020 1014:8021 1014:8022 1014:8023 1015:8018 1015:8019 1015:8020 1015:8021 1015:8022 1015:8023 1016:8018 1016:8019 1016:8020 1016:8021 1016:8022 1016:8023 2001:8018 2001:8019 2001:8020 2001:8021 2001:8022 2001:8023 2002:8018 2002:8019 2002:8020 2002:8021 2002:8022 2002:8023 2003:8018 2003:8019 2003:8020 2003:8021 2003:8022 2003:8023 2004:8018 2004:8019 2004:8020 2004:8021 2004:8022 2004:8023 2005:8018 2005:8019 2005:8020 2005:8021 2005:8022 2005:8023 2006:8018 2006:8019 2006:8020 2006:8021 2006:8022 2006:8023 2007:8018 2007:8019 2007:8020 2007:8021 2007:8022 2007:8023 2008:8018 2008:8019 2008:8020 2008:8021 2008:8022 2008:8023 2009:8018 2009:8019 2009:8020 2009:8021 2009:8022 2009:8023 2010:8018 2010:8019 2010:8020 2010:8021 2010:8022 2010:8023 2011:8018 2011:8019 2011:8020 2011:8021 2011:8022 2011:8023 2012:8018 2012:8019 2012:8020 2012:8021 2012:8022 2012:8023 3001:8018 3001:8019 3001:8020 3001:8021 3001:8022 3001:8023 3002:8018 3002:8019 3002:8020 3002:8021 3002:8022 3002:8023 3003:8018 3003:8019 3003:8020 3003:8021 3003:8022 3003:8023 3004:8018 3004:8019 3004:8020 3004:8021 3004:8022 3004:8023 3005:8018 3005:8019 3005:8020 3005:8021 3005:8022 3005:8023 3006:8018 3006:8019 3006:8020 3006:8021 3006:8022 3006:8023 3007:8018 3007:8019 3007:8020 3007:8021 3007:8022 3007:8023 3008:8018 3008:8019 3008:8020 3008:8021 3008:8022 3008:8023 3009:8018 3009:8019 3009:8020 3009:8021 3009:8022 3009:8023 3010:8018 3010:8019 3010:8020 3010:8021 3010:8022 3010:8023 3011:8018 3011:8019 3011:8020 3011:8021 3011:8022 3011:8023 3012:8018 3012:8019 3012:8020 3012:8021 3012:8022 3012:8023 3013:8018 3013:8019 3013:8020 3013:8021 3013:8022 3013:8023 3014:8018 3014:8019 3014:8020 3014:8021 3014:8022 3014:8023 1001:8024 1001:8025 1001:8026 1001:8027 — — 1002:8024 1002:8025 1002:8026 1002:8027 1003:8024 1003:8025 1003:8026 1003:8027 1004:8024 1004:8025 1004:8026 1004:8027 1005:8024 1005:8025 1005:8026 1005:8027 1006:8024 1006:8025 1006:8026 1006:8027 1007:8024 1007:8025 1007:8026 1007:8027 1008:8024 1008:8025 1008:8026 1008:8027 1009:8024 1009:8025 1009:8026 1009:8027 1010:8024 1010:8025 1010:8026 1010:8027 1011:8024 1011:8025 1011:8026 1011:8027 1012:8024 1012:8025 1012:8026 1012:8027 1013:8024 1013:8025 1013:8026 1013:8027 1014:8024 1014:8025 1014:8026 1014:8027 1015:8024 1015:8025 1015:8026 1015:8027 1016:8024 1016:8025 1016:8026 1016:8027 2001:8024 2001:8025 2001:8026 2001:8027 2002:8024 2002:8025 2002:8026 2002:8027 2003:8024 2003:8025 2003:8026 2003:8027 2004:8024 2004:8025 2004:8026 2004:8027 2005:8024 2005:8025 2005:8026 2005:8027 2006:8024 2006:8025 2006:8026 2006:8027 2007:8024 2007:8025 2007:8026 2007:8027 2008:8024 2008:8025 2008:8026 2008:8027 2009:8024 2009:8025 2009:8026 2009:8027 2010:8024 2010:8025 2010:8026 2010:8027 2011:8024 2011:8025 2011:8026 2011:8027 2012:8024 2012:8025 2012:8026 2012:8027 3001:8024 3001:8025 3001:8026 3001:8027 3002:8024 3002:8025 3002:8026 3002:8027 3003:8024 3003:8025 3003:8026 3003:8027 3004:8024 3004:8025 3004:8026 3004:8027 3005:8024 3005:8025 3005:8026 3005:8027 3006:8024 3006:8025 3006:8026 3006:8027 3007:8024 3007:8025 3007:8026 3007:8027 3008:8024 3008:8025 3008:8026 3008:8027 3009:8024 3009:8025 3009:8026 3009:8027 3010:8024 3010:8025 3010:8026 3010:8027 3011:8024 3011:8025 3011:8026 3011:8027 3012:8024 3012:8025 3012:8026 3012:8027 3013:8024 3013:8025 3013:8026 3013:8027 3014:8024 3014:8025 3014:8026 3014:8027

TABLE B Example combinations of a compound X with a compound Y. X:Y X:Y X:Y X:Y X:Y X:Y 4001:8000 4001:8001 4001:8002 4001:8003 4001:8004 4001:8005 4002:8000 4002:8001 4002:8002 4002:8003 4002:8004 4002:8005 4003:8000 4003:8001 4003:8002 4003:8003 4003:8004 4003:8005 4004:8000 4004:8001 4004:8002 4004:8003 4004:8004 4004:8005 4005:8000 4005:8001 4005:8002 4005:8003 4005:8004 4005:8005 4006:8000 4006:8001 4006:8002 4006:8003 4006:8004 4006:8005 4007:8000 4007:8001 4007:8002 4007:8003 4007:8004 4007:8005 4008:8000 4008:8001 4008:8002 4008:8003 4008:8004 4008:8005 4009:8000 4009:8001 4009:8002 4009:8003 4009:8004 4009:8005 4010:8000 4010:8001 4010:8002 4010:8003 4010:8004 4010:8005 4011:8000 4011:8001 4011:8002 4011:8003 4011:8004 4011:8005 4012:8000 4012:8001 4012:8002 4012:8003 4012:8004 4012:8005 5001:8000 5001:8001 5001:8002 5001:8003 5001:8004 5001:8005 5002:8000 5002:8001 5002:8002 5002:8003 5002:8004 5002:8005 5003:8000 5003:8001 5003:8002 5003:8003 5003:8004 5003:8005 5004:8000 5004:8001 5004:8002 5004:8003 5004:8004 5004:8005 5005:8000 5005:8001 5005:8002 5005:8003 5005:8004 5005:8005 5006:8000 5006:8001 5006:8002 5006:8003 5006:8004 5006:8005 5007:8000 5007:8001 5007:8002 5007:8003 5007:8004 5007:8005 5008:8000 5008:8001 5008:8002 5008:8003 5008:8004 5008:8005 5009:8000 5009:8001 5009:8002 5009:8003 5009:8004 5009:8005 5010:8000 5010:8001 5010:8002 5010:8003 5010:8004 5010:8005 5011:8000 5011:8001 5011:8002 5011:8003 5011:8004 5011:8005 4001:8006 4001:8007 4001:8008 4001:8009 4001:8010 4001:8011 4002:8006 4002:8007 4002:8008 4002:8009 4002:8010 4002:8011 4003:8006 4003:8007 4003:8008 4003:8009 4003:8010 4003:8011 4004:8006 4004:8007 4004:8008 4004:8009 4004:8010 4004:8011 4005:8006 4005:8007 4005:8008 4005:8009 4005:8010 4005:8011 4006:8006 4006:8007 4006:8008 4006:8009 4006:8010 4006:8011 4007:8006 4007:8007 4007:8008 4007:8009 4007:8010 4007:8011 4008:8006 4008:8007 4008:8008 4008:8009 4008:8010 4008:8011 4009:8006 4009:8007 4009:8008 4009:8009 4009:8010 4009:8011 4010:8006 4010:8007 4010:8008 4010:8009 4010:8010 4010:8011 4011:8006 4011:8007 4011:8008 4011:8009 4011:8010 4011:8011 4012:8006 4012:8007 4012:8008 4012:8009 4012:8010 4012:8011 5001:8006 5001:8007 5001:8008 5001:8009 5001:8010 5001:8011 5002:8006 5002:8007 5002:8008 5002:8009 5002:8010 5002:8011 5003:8006 5003:8007 5003:8008 5003:8009 5003:8010 5003:8011 5004:8006 5004:8007 5004:8008 5004:8009 5004:8010 5004:8011 5005:8006 5005:8007 5005:8008 5005:8009 5005:8010 5005:8011 5006:8006 5006:8007 5006:8008 5006:8009 5006:8010 5006:8011 5007:8006 5007:8007 5007:8008 5007:8009 5007:8010 5007:8011 5008:8006 5008:8007 5008:8008 5008:8009 5008:8010 5008:8011 5009:8006 5009:8007 5009:8008 5009:8009 5009:8010 5009:8011 5010:8006 5010:8007 5010:8008 5010:8009 5010:8010 5010:8011 5011:8006 5011:8007 5011:8008 5011:8009 5011:8010 5011:8011 4001:8012 4001:8013 4001:8014 4001:8015 4001:8016 4001:8017 4002:8012 4002:8013 4002:8014 4002:8015 4002:8016 4002:8017 4003:8012 4003:8013 4003:8014 4003:8015 4003:8016 4003:8017 4004:8012 4004:8013 4004:8014 4004:8015 4004:8016 4004:8017 4005:8012 4005:8013 4005:8014 4005:8015 4005:8016 4005:8017 4006:8012 4006:8013 4006:8014 4006:8015 4006:8016 4006:8017 4007:8012 4007:8013 4007:8014 4007:8015 4007:8016 4007:8017 4008:8012 4008:8013 4008:8014 4008:8015 4008:8016 4008:8017 4009:8012 4009:8013 4009:8014 4009:8015 4009:8016 4009:8017 4010:8012 4010:8013 4010:8014 4010:8015 4010:8016 4010:8017 4011:8012 4011:8013 4011:8014 4011:8015 4011:8016 4011:8017 4012:8012 4012:8013 4012:8014 4012:8015 4012:8016 4012:8017 5001:8012 5001:8013 5001:8014 5001:8015 5001:8016 5001:8017 5002:8012 5002:8013 5002:8014 5002:8015 5002:8016 5002:8017 5003:8012 5003:8013 5003:8014 5003:8015 5003:8016 5003:8017 5004:8012 5004:8013 5004:8014 5004:8015 5004:8016 5004:8017 5005:8012 5005:8013 5005:8014 5005:8015 5005:8016 5005:8017 5006:8012 5006:8013 5006:8014 5006:8015 5006:8016 5006:8017 5007:8012 5007:8013 5007:8014 5007:8015 5007:8016 5007:8017 5008:8012 5008:8013 5008:8014 5008:8015 5008:8016 5008:8017 5009:8012 5009:8013 5009:8014 5009:8015 5009:8016 5009:8017 5010:8012 5010:8013 5010:8014 5010:8015 5010:8016 5010:8017 5011:8012 5011:8013 5011:8014 5011:8015 5011:8016 5011:8017 4001:8018 4001:8019 4001:8020 4001:8021 4001:8022 4001:8023 4002:8018 4002:8019 4002:8020 4002:8021 4002:8022 4002:8023 4003:8018 4003:8019 4003:8020 4003:8021 4003:8022 4003:8023 4004:8018 4004:8019 4004:8020 4004:8021 4004:8022 4004:8023 4005:8018 4005:8019 4005:8020 4005:8021 4005:8022 4005:8023 4006:8018 4006:8019 4006:8020 4006:8021 4006:8022 4006:8023 4007:8018 4007:8019 4007:8020 4007:8021 4007:8022 4007:8023 4008:8018 4008:8019 4008:8020 4008:8021 4008:8022 4008:8023 4009:8018 4009:8019 4009:8020 4009:8021 4009:8022 4009:8023 4010:8018 4010:8019 4010:8020 4010:8021 4010:8022 4010:8023 4011:8018 4011:8019 4011:8020 4011:8021 4011:8022 4011:8023 4012:8018 4012:8019 4012:8020 4012:8021 4012:8022 4012:8023 5001:8018 5001:8019 5001:8020 5001:8021 5001:8022 5001:8023 5002:8018 5002:8019 5002:8020 5002:8021 5002:8022 5002:8023 5003:8018 5003:8019 5003:8020 5003:8021 5003:8022 5003:8023 5004:8018 5004:8019 5004:8020 5004:8021 5004:8022 5004:8023 5005:8018 5005:8019 5005:8020 5005:8021 5005:8022 5005:8023 5006:8018 5006:8019 5006:8020 5006:8021 5006:8022 5006:8023 5007:8018 5007:8019 5007:8020 5007:8021 5007:8022 5007:8023 5008:8018 5008:8019 5008:8020 5008:8021 5008:8022 5008:8023 5009:8018 5009:8019 5009:8020 5009:8021 5009:8022 5009:8023 5010:8018 5010:8019 5010:8020 5010:8021 5010:8022 5010:8023 5011:8018 5011:8019 5011:8020 5011:8021 5011:8022 5011:8023 4001:8024 4001:8025 4001:8026 4001:8027 — — 4002:8024 4002:8025 4002:8026 4002:8027 4003:8024 4003:8025 4003:8026 4003:8027 4004:8024 4004:8025 4004:8026 4004:8027 4005:8024 4005:8025 4005:8026 4005:8027 4006:8024 4006:8025 4006:8026 4006:8027 4007:8024 4007:8025 4007:8026 4007:8027 4008:8024 4008:8025 4008:8026 4008:8027 4009:8024 4009:8025 4009:8026 4009:8027 4010:8024 4010:8025 4010:8026 4010:8027 4011:8024 4011:8025 4011:8026 4011:8027 4012:8024 4012:8025 4012:8026 4012:8027 5001:8024 5001:8025 5001:8026 5001:8027 5002:8024 5002:8025 5002:8026 5002:8027 5003:8024 5003:8025 5003:8026 5003:8027 5004:8024 5004:8025 5004:8026 5004:8027 5005:8024 5005:8025 5005:8026 5005:8027 5006:8024 5006:8025 5006:8026 5006:8027 5007:8024 5007:8025 5007:8026 5007:8027 5008:8024 5008:8025 5008:8026 5008:8027 5009:8024 5009:8025 5009:8026 5009:8027 5010:8024 5010:8025 5010:8026 5010:8027 5011:8024 5011:8025 5011:8026 5011:8027

TABLE C Example combinations of a compound X with a compound Y. X:Y X:Y X:Y X:Y X:Y X:Y 6000:8000 6043:8000 6000:8001 6043:8001 6000:8002 6043:8002 6001:8000 6044:8000 6001:8001 6044:8001 6001:8002 6044:8002 6002:8000 6045:8000 6002:8001 6045:8001 6002:8002 6045:8002 6003:8000 6046:8000 6003:8001 6046:8001 6003:8002 6046:8002 6004:8000 6047:8000 6004:8001 6047:8001 6004:8002 6047:8002 6005:8000 6048:8000 6005:8001 6048:8001 6005:8002 6048:8002 6006:8000 6049:8000 6006:8001 6049:8001 6006:8002 6049:8002 6007:8000 6050:8000 6007:8001 6050:8001 6007:8002 6050:8002 6008:8000 6051:8000 6008:8001 6051:8001 6008:8002 6051:8002 6009:8000 6052:8000 6009:8001 6052:8001 6009:8002 6052:8002 6010:8000 6053:8000 6010:8001 6053:8001 6010:8002 6053:8002 6011:8000 6054:8000 6011:8001 6054:8001 6011:8002 6054:8002 6012:8000 6055:8000 6012:8001 6055:8001 6012:8002 6055:8002 6013:8000 6056:8000 6013:8001 6056:8001 6013:8002 6056:8002 6014:8000 6057:8000 6014:8001 6057:8001 6014:8002 6057:8002 6015:8000 6058:8000 6015:8001 6058:8001 6015:8002 6058:8002 6016:8000 6059:8000 6016:8001 6059:8001 6016:8002 6059:8002 6017:8000 6060:8000 6017:8001 6060:8001 6017:8002 6060:8002 6018:8000 6061:8000 6018:8001 6061:8001 6018:8002 6061:8002 6019:8000 6062:8000 6019:8001 6062:8001 6019:8002 6062:8002 6020:8000 6063:8000 6020:8001 6063:8001 6020:8002 6063:8002 6021:8000 6064:8000 6021:8001 6064:8001 6021:8002 6064:8002 6022:8000 6065:8000 6022:8001 6065:8001 6022:8002 6065:8002 6023:8000 6066:8000 6023:8001 6066:8001 6023:8002 6066:8002 6024:8000 6067:8000 6024:8001 6067:8001 6024:8002 6067:8002 6025:8000 6068:8000 6025:8001 6068:8001 6025:8002 6068:8002 6026:8000 6069:8000 6026:8001 6069:8001 6026:8002 6069:8002 6027:8000 6070:8000 6027:8001 6070:8001 6027:8002 6070:8002 6028:8000 6071:8000 6028:8001 6071:8001 6028:8002 6071:8002 6029:8000 6072:8000 6029:8001 6072:8001 6029:8002 6072:8002 6030:8000 6073:8000 6030:8001 6073:8001 6030:8002 6073:8002 6031:8000 6074:8000 6031:8001 6074:8001 6031:8002 6074:8002 6032:8000 6075:8000 6032:8001 6075:8001 6032:8002 6075:8002 6033:8000 6076:8000 6033:8001 6076:8001 6033:8002 6076:8002 6034:8000 6077:8000 6034:8001 6077:8001 6034:8002 6077:8002 6035:8000 6078:8000 6035:8001 6078:8001 6035:8002 6078:8002 6036:8000 6036:8001 6036:8002 6037:8000 6037:8001 6037:8002 6038:8000 6038:8001 6038:8002 6039:8000 6039:8001 6039:8002 6040:8000 6040:8001 6040:8002 6041:8000 6041:8001 6041:8002 6042:8000 6042:8001 6042:8002 6000:8003 6043:8003 6000:8005 6043:8005 6000:8005 6043:8005 6001:8003 6044:8003 6001:8005 6044:8005 6001:8005 6044:8005 6002:8003 6045:8003 6002:8005 6045:8005 6002:8005 6045:8005 6003:8003 6046:8003 6003:8005 6046:8005 6003:8005 6046:8005 6004:8003 6047:8003 6004:8005 6047:8005 6004:8005 6047:8005 6005:8003 6048:8003 6005:8005 6048:8005 6005:8005 6048:8005 6006:8003 6049:8003 6006:8005 6049:8005 6006:8005 6049:8005 6007:8003 6050:8003 6007:8005 6050:8005 6007:8005 6050:8005 6008:8003 6051:8003 6008:8005 6051:8005 6008:8005 6051:8005 6009:8003 6052:8003 6009:8005 6052:8005 6009:8005 6052:8005 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6043:8024 6000:8025 6043:8025 6000:8026 6043:8026 6001:8024 6044:8024 6001:8025 6044:8025 6001:8026 6044:8026 6002:8024 6045:8024 6002:8025 6045:8025 6002:8026 6045:8026 6003:8024 6046:8024 6003:8025 6046:8025 6003:8026 6046:8026 6004:8024 6047:8024 6004:8025 6047:8025 6004:8026 6047:8026 6005:8024 6048:8024 6005:8025 6048:8025 6005:8026 6048:8026 6006:8024 6049:8024 6006:8025 6049:8025 6006:8026 6049:8026 6007:8024 6050:8024 6007:8025 6050:8025 6007:8026 6050:8026 6008:8024 6051:8024 6008:8025 6051:8025 6008:8026 6051:8026 6009:8024 6052:8024 6009:8025 6052:8025 6009:8026 6052:8026 6010:8024 6053:8024 6010:8025 6053:8025 6010:8026 6053:8026 6011:8024 6054:8024 6011:8025 6054:8025 6011:8026 6054:8026 6012:8024 6055:8024 6012:8025 6055:8025 6012:8026 6055:8026 6013:8024 6056:8024 6013:8025 6056:8025 6013:8026 6056:8026 6014:8024 6057:8024 6014:8025 6057:8025 6014:8026 6057:8026 6015:8024 6058:8024 6015:8025 6058:8025 6015:8026 6058:8026 6016:8024 6059:8024 6016:8025 6059:8025 6016:8026 6059:8026 6017:8024 6060:8024 6017:8025 6060:8025 6017:8026 6060:8026 6018:8024 6061:8024 6018:8025 6061:8025 6018:8026 6061:8026 6019:8024 6062:8024 6019:8025 6062:8025 6019:8026 6062:8026 6020:8024 6063:8024 6020:8025 6063:8025 6020:8026 6063:8026 6021:8024 6064:8024 6021:8025 6064:8025 6021:8026 6064:8026 6022:8024 6065:8024 6022:8025 6065:8025 6022:8026 6065:8026 6023:8024 6066:8024 6023:8025 6066:8025 6023:8026 6066:8026 6024:8024 6067:8024 6024:8025 6067:8025 6024:8026 6067:8026 6025:8024 6068:8024 6025:8025 6068:8025 6025:8026 6068:8026 6026:8024 6069:8024 6026:8025 6069:8025 6026:8026 6069:8026 6027:8024 6070:8024 6027:8025 6070:8025 6027:8026 6070:8026 6028:8024 6071:8024 6028:8025 6071:8025 6028:8026 6071:8026 6029:8024 6072:8024 6029:8025 6072:8025 6029:8026 6072:8026 6030:8024 6073:8024 6030:8025 6073:8025 6030:8026 6073:8026 6031:8024 6074:8024 6031:8025 6074:8025 6031:8026 6074:8026 6032:8024 6075:8024 6032:8025 6075:8025 6032:8026 6075:8026 6033:8024 6076:8024 6033:8025 6076:8025 6033:8026 6076:8026 6034:8024 6077:8024 6034:8025 6077:8025 6034:8026 6077:8026 6035:8024 6078:8024 6035:8025 6078:8025 6035:8026 6078:8026 6036:8024 6036:8025 6036:8026 6037:8024 6037:8025 6037:8026 6038:8024 6038:8025 6038:8026 6039:8024 6039:8025 6039:8026 6040:8024 6040:8025 6040:8026 6041:8024 6041:8025 6041:8026 6042:8024 6042:8025 6042:8026 6000:8027 6043:8027 — — — — 6001:8027 6044:8027 6002:8027 6045:8027 6003:8027 6046:8027 6004:8027 6047:8027 6005:8027 6048:8027 6006:8027 6049:8027 6007:8027 6050:8027 6008:8027 6051:8027 6009:8027 6052:8027 6010:8027 6053:8027 6011:8027 6054:8027 6012:8027 6055:8027 6013:8027 6056:8027 6014:8027 6057:8027 6015:8027 6058:8027 6016:8027 6059:8027 6017:8027 6060:8027 6018:8027 6061:8027 6019:8027 6062:8027 6020:8027 6063:8027 6021:8027 6064:8027 6022:8027 6065:8027 6023:8027 6066:8027 6024:8027 6067:8027 6025:8027 6068:8027 6026:8027 6069:8027 6027:8027 6070:8027 6028:8027 6071:8027 6029:8027 6072:8027 6030:8027 6073:8027 6031:8027 6074:8027 6032:8027 6075:8027 6033:8027 6076:8027 6034:8027 6077:8027 6035:8027 6078:8027 6036:8027 6037:8027 6038:8027 6039:8027 6040:8027 6041:8027 6042:8027

TABLE D Example combinations of a compound X with a compound Y. X:Y X:Y X:Y X:Y X:Y X:Y 7000:8000 7000:8001 7000:8002 7000:8003 7000:8004 7000:8005 7001:8000 7001:8001 7001:8002 7001:8003 7001:8004 7001:8005 7002:8000 7002:8001 7002:8002 7002:8003 7002:8004 7002:8005 7003:8000 7003:8001 7003:8002 7003:8003 7003:8004 7003:8005 7004:8000 7004:8001 7004:8002 7004:8003 7004:8004 7004:8005 7005:8000 7005:8001 7005:8002 7005:8003 7005:8004 7005:8005 7006:8000 7006:8001 7006:8002 7006:8003 7006:8004 7006:8005 7007:8000 7007:8001 7007:8002 7007:8003 7007:8004 7007:8005 7008:8000 7008:8001 7008:8002 7008:8003 7008:8004 7008:8005 7009:8000 7009:8001 7009:8002 7009:8003 7009:8004 7009:8005 7010:8000 7010:8001 7010:8002 7010:8003 7010:8004 7010:8005 7011:8000 7011:8001 7011:8002 7011:8003 7011:8004 7011:8005 7012:8000 7012:8001 7012:8002 7012:8003 7012:8004 7012:8005 7013:8000 7013:8001 7013:8002 7013:8003 7013:8004 7013:8005 7014:8000 7014:8001 7014:8002 7014:8003 7014:8004 7014:8005 7015:8000 7015:8001 7015:8002 7015:8003 7015:8004 7015:8005 7016:8000 7016:8001 7016:8002 7016:8003 7016:8004 7016:8005 7000:8006 7000:8007 7000:8008 7000:8009 7000:8010 7000:8011 7001:8006 7001:8007 7001:8008 7001:8009 7001:8010 7001:8011 7002:8006 7002:8007 7002:8008 7002:8009 7002:8010 7002:8011 7003:8006 7003:8007 7003:8008 7003:8009 7003:8010 7003:8011 7004:8006 7004:8007 7004:8008 7004:8009 7004:8010 7004:8011 7005:8006 7005:8007 7005:8008 7005:8009 7005:8010 7005:8011 7006:8006 7006:8007 7006:8008 7006:8009 7006:8010 7006:8011 7007:8006 7007:8007 7007:8008 7007:8009 7007:8010 7007:8011 7008:8006 7008:8007 7008:8008 7008:8009 7008:8010 7008:8011 7009:8006 7009:8007 7009:8008 7009:8009 7009:8010 7009:8011 7010:8006 7010:8007 7010:8008 7010:8009 7010:8010 7010:8011 7011:8006 7011:8007 7011:8008 7011:8009 7011:8010 7011:8011 7012:8006 7012:8007 7012:8008 7012:8009 7012:8010 7012:8011 7013:8006 7013:8007 7013:8008 7013:8009 7013:8010 7013:8011 7014:8006 7014:8007 7014:8008 7014:8009 7014:8010 7014:8011 7015:8006 7015:8007 7015:8008 7015:8009 7015:8010 7015:8011 7016:8006 7016:8007 7016:8008 7016:8009 7016:8010 7016:8011 7000:8012 7000:8013 7000:8014 7000:8015 7000:8016 7000:8017 7001:8012 7001:8013 7001:8014 7001:8015 7001:8016 7001:8017 7002:8012 7002:8013 7002:8014 7002:8015 7002:8016 7002:8017 7003:8012 7003:8013 7003:8014 7003:8015 7003:8016 7003:8017 7004:8012 7004:8013 7004:8014 7004:8015 7004:8016 7004:8017 7005:8012 7005:8013 7005:8014 7005:8015 7005:8016 7005:8017 7006:8012 7006:8013 7006:8014 7006:8015 7006:8016 7006:8017 7007:8012 7007:8013 7007:8014 7007:8015 7007:8016 7007:8017 7008:8012 7008:8013 7008:8014 7008:8015 7008:8016 7008:8017 7009:8012 7009:8013 7009:8014 7009:8015 7009:8016 7009:8017 7010:8012 7010:8013 7010:8014 7010:8015 7010:8016 7010:8017 7011:8012 7011:8013 7011:8014 7011:8015 7011:8016 7011:8017 7012:8012 7012:8013 7012:8014 7012:8015 7012:8016 7012:8017 7013:8012 7013:8013 7013:8014 7013:8015 7013:8016 7013:8017 7014:8012 7014:8013 7014:8014 7014:8015 7014:8016 7014:8017 7015:8012 7015:8013 7015:8014 7015:8015 7015:8016 7015:8017 7016:8012 7016:8013 7016:8014 7016:8015 7016:8016 7016:8017 7000:8018 7000:8019 7000:8020 7000:8021 7000:8022 7000:8023 7001:8018 7001:8019 7001:8020 7001:8021 7001:8022 7001:8023 7002:8018 7002:8019 7002:8020 7002:8021 7002:8022 7002:8023 7003:8018 7003:8019 7003:8020 7003:8021 7003:8022 7003:8023 7004:8018 7004:8019 7004:8020 7004:8021 7004:8022 7004:8023 7005:8018 7005:8019 7005:8020 7005:8021 7005:8022 7005:8023 7006:8018 7006:8019 7006:8020 7006:8021 7006:8022 7006:8023 7007:8018 7007:8019 7007:8020 7007:8021 7007:8022 7007:8023 7008:8018 7008:8019 7008:8020 7008:8021 7008:8022 7008:8023 7009:8018 7009:8019 7009:8020 7009:8021 7009:8022 7009:8023 7010:8018 7010:8019 7010:8020 7010:8021 7010:8022 7010:8023 7011:8018 7011:8019 7011:8020 7011:8021 7011:8022 7011:8023 7012:8018 7012:8019 7012:8020 7012:8021 7012:8022 7012:8023 7013:8018 7013:8019 7013:8020 7013:8021 7013:8022 7013:8023 7014:8018 7014:8019 7014:8020 7014:8021 7014:8022 7014:8023 7015:8018 7015:8019 7015:8020 7015:8021 7015:8022 7015:8023 7016:8018 7016:8019 7016:8020 7016:8021 7016:8022 7016:8023 7000:8024 7000:8025 7000:8026 7000:8027 — — 7001:8024 7001:8025 7001:8026 7001:8027 7002:8024 7002:8025 7002:8026 7002:8027 7003:8024 7003:8025 7003:8026 7003:8027 7004:8024 7004:8025 7004:8026 7004:8027 7005:8024 7005:8025 7005:8026 7005:8027 7006:8024 7006:8025 7006:8026 7006:8027 7007:8024 7007:8025 7007:8026 7007:8027 7008:8024 7008:8025 7008:8026 7008:8027 7009:8024 7009:8025 7009:8026 7009:8027 7010:8024 7010:8025 7010:8026 7010:8027 7011:8024 7011:8025 7011:8026 7011:8027 7012:8024 7012:8025 7012:8026 7012:8027 7013:8024 7013:8025 7013:8026 7013:8027 7014:8024 7014:8025 7014:8026 7014:8027 7015:8024 7015:8025 7015:8026 7015:8027 7016:8024 7016:8025 7016:8026 7016:8027

EXAMPLES

Additional embodiments are disclosed in further detail in the following examples, which are not in any way intended to limit the scope of the claims.

Example 1 Compound 1a

Step 1: Compound P1-2

To a solution of Dess-Martin periodinane (12.0 g, 28.1 mmol) in 500 mL of CH₂Cl₂ (DCM) was added P1-1 (8.0 g, 17.3 mmol) at 0° C. The mixture was warmed to room temperature and stirred for 12 hours. The solvent was removed in vacuo, and the residue was triturated with methyl tert-butyl ether (TBME) (150 mL) and filtered through a pad of MgSO₄. The filtrate was stirred with an equal volume of Na₂S₂O₃.5H₂O in 50 mL of saturated NaHCO₃ until the organic layer became clear (˜10 minutes). The organic layer was separated, washed with brine, dried over MgSO₄, and concentrated to give P1-2 as a white solid (7.3 g, 91%).

Step 2: Compound P1-3

To a solution of P1-2 (39.0 g, 84.9 mmol) in anhydrous THF (450 mL) was added ethynylmagnesium bromide (390 mL, 195 mmol) dropwise over 20 minutes at −78° C. using an ice-acetone cooling bath. The resulting mixture was stirred for 2 hours at −78° C. The ice-acetone cooling bath was removed and saturated NH₄Cl (600 mL) was added with stirring. After warming to room temperature, the mixture was filtered through CELITE™ and washed with saturated aqueous NH₄Cl (300 mL). The combined organic phase was dried with Na₂SO₄, filtered, and concentrated to provide a crude product (38.0 g). The crude product was dissolved in anhydrous CH₂Cl₂ (DCM) (200 mL), followed by addition of 4-dimethylaminopyridine (DMAP) (19.1 g, 156.4 mmol), benzoyl chloride (23.5 g, 156.4 mmol) and Et₃N (23.7 g, 234.6 mmol). After stirring for 12 hours at room temperature, the reaction mixture was diluted with DCM (100 mL) and then washed with saturated aqueous NaHCO₃ (100 mL). The combined aqueous phase was extracted with DCM (100 mL) and the combined organic phase was dried with Na₂SO₄, filtered, and evaporated to dryness under reduced pressure to give a yellow oil. The oil was purified by column chromatography (5% ethyl acetate in petroleum ether) to give P1-3 (18.0 g, 39%).

Step 3: Compound P1-4

To a suspension of uracil (4.6 g, 40.6 mmol) in 20 mL of distilled acetonitrile was added N,O-bis(trimethylsilyl) acetamide (16.6 g, 81.3 mmol). The resulting solution was refluxed for 30 minutes and then cooled to ambient temperature. A solution of P1-3 (12.0 g, 20.34 mmol) in 10 mL of acetonitrile was added, followed by dropwise addition of SnCl₄ (21.15 g, 81.3 mmol). The reaction mixture was refluxed overnight. The reaction mixture was cooled to room temperature, diluted with 100 mL of ethyl acetate and washed with saturated NaHCO₃ and brine. The organic layer was dried with Na₂SO₄, filtered, and concentrated. The resulting residue was purified by silica gel column chromatography (ethyl acetate/hexanes 5:1) to give a protected nucleoside intermediate (7.6 g, yield 64%) as a white solid. The nucleoside intermediate was dissolved in methanolic ammonia (70 mL, saturated) and the mixture was stirred at room temperature for 14 hours. The solvent was removed and the residue was purified by silica gel column chromatography (DCM/MeOH=30:1 to 10:1) to give P1-4 as a white solid (1.9 g, 56%). ¹H NMR (CD₃OD, 400 MHz) δ 8.05 (d, J=8.0 Hz, 1H), 6.02 (s, 1H), 5.68 (d, J=8.0 Hz, 1H), 4.19 (d, J=8.8 Hz, 1H), 3.93 (dd, J₁=2.4 Hz, J₂=12.4 Hz, 1H), 3.88-3.92 (m, 1H), 3.76 (dd, J₁=2.8 Hz, J₂=12.8 Hz, 1H), 3.02 (s, 1H); EST-TOF-MS: m/z 291 [M+Na]⁺.

Step 4: Compound 1a

To a suspension of P1-4 (110 mg, 0.41 mmol) in dry THF (2 mL) were added N-methylimidazole (NMI) (0.2 mL) and (2S)-isopropyl 2-((chloro(phenoxy)phosphorothioyl)amino)propanoate (389 mg, 1.2 mmol). The reaction mixture was heated to 70° C. and stirred for 1 hour. The solvents were evaporated and the resulting residue was purified by RP HPLC (MeCN and 0.1% HCOOH in water) to give compound 1a as a white solid (a mixture of 2 P-isomers, 100 mg, 44%). ¹H NMR (MeOD, 400 MHz) δ 7.79, 7.71 (2d, J=8.0 Hz, 1H), 7.15-7.34 (m, 5H), 6.06, 6.03 (2s, 1H), 5.59, 5.56 (2d, J=8.0 Hz, 1H), 4.94-5.01 (m, 1H), 4.46-4.52 (m, 1H), 4.37-4.39 (m, 1H), 4.18-4.32 (m, 1H), 4.05-4.16 (m, 2H), 3.05, 3.27 (2s, 1H), 1.36, 1.31 (2d, J=0.8 Hz, 3H), 1.21-1.24 (m, 6H). ³¹P NMR (CD₃OD, 162 MHz) δ 68.45, 68.26. ESI-LCMS: m/z 554.0 [M+H]⁺.

The two diastereomers were separated to provide 1aa and 1ab as follows. A 60:40 diastereomeric mixture of compound 1a (974 mg) was subjected to chromatography using a 30×250 mm 5μ Chiracel OZ-H column and eluted with methanol. There was obtained 522 mg of the faster eluting diastereomer (3.95 min), which was present in slight excess in the mixture. There was obtained 334 mg of the slower eluting diastereomer (5.24 min). Faster eluting diastereomer, major isomer: HPLC purity >99.5%, ³¹P NMR 67.1, LC/MS 552 (M-1). Slower eluting diastereomer, minor isomer: HPLC purity >99.3%, ³¹P NMR 67.9, LC/MS 552 (M-1).

Example 2 Compound 2a

Step 1: Compound P2-1

To a stirred solution of P1-2 (6.0 g, 12.8 mmol) in THF (20 mL) was added vinylmagnesium bromide (44.8 mL, 44.8 mmol) dropwise over 10 minutes and the resulting mixture was stirred at −78° C. for 2 hours. The reaction was quenched with saturated NH₄Cl (100 mL), and the mixture was filtered through CELITE™ and extracted with ethyl acetate. The combined organic phase was dried with Na₂SO₄, filtered, and concentrated to give a crude intermediate. The crude intermediate was dissolved in anhydrous DCM (150 mL), followed by addition of dimethylaminopyridine (DMAP) (3.49 g, 28.6 mmol), benzoyl chloride (6.5 mL, 42.9 mmol) and Et₃N (6.0 mL, 42.9 mmol). After stirring at room temperature for 12 hours, the reaction mixture was diluted with DCM (DCM) (100 mL), and washed successively with 1 M aqueous HCl (3×100 mL) and saturated aqueous NaHCO₃ (50 mL). The combined organic phase was dried with Na₂SO₄, filtered, and evaporated to give a residue. The residue was purified by column chromatography (5% ethyl acetate in petroleum ether) to give P2-1 as a white solid (2.3 g, 27%).

Step 3: Compound P2-2

To a suspension of uracil (851 mg, 7.6 mmol) in 20 mL of distilled acetonitrile was added N,O-bis(trimethylsilyl) acetamide (3.1 g, 15.2 mmol). The resulting solution was brought to reflux for 30 minutes. The solution was cooled to ambient temperature. A solution of P2-1 (2.3 g, 3.8 mmol) in 20 mL of acetonitrile was added, followed by slow dropwise addition of SnCl₄ (4.0 g, 15.2 mmol). The reaction mixture was refluxed overnight. The reaction mixture was diluted with 200 mL of ethyl acetate, and washed with saturated NaHCO₃ and brine. The organic layer was dried with Na₂SO₄, filtered, and concentrated to give a residue. The residue was purified by silica gel column chromatography (ethyl acetate/hexanes 8:1) to afford the protected nucleoside as a white solid (560 mg, 26%). The protected nucleoside (560 mg, 0.96 mmol) was dissolved in methanolic ammonia (20 mL, saturated) and the mixture was stirred at room temperature for 14 hours. The solvent was removed, and the residue was purified by silica gel column chromatography (DCM/MeOH=30:1 to 10:1) to give P2-2 as a white solid (230 mg, 88%). ¹H NMR (CD₃OD, 400 MHz) δ 8.11 (d, J=8.0 Hz, 1H), 5.94 (s, 1H), 5.65-5.71 (m, 2H), 5.43 (dd, J₁=1.2 Hz, J₂=17.2 Hz, 1H), 5.24 (d, J₁=1.2 Hz, J₂=10.8 Hz, 1H), 4.21 (d, J=8.8 Hz, 1H), 3.97-4.01 (m, 2H), 3.78-3.82 (m, 1H). ESI-MS: m/z 271 [M+H]⁺.

Step 4: Compound 2a

To a suspension of P2-2 (110 mg, 0.41 mmol) in dry tetrahydrofuran (THF) (2 mL) were added N-methylimidazole (NMI) (0.2 mL) and (2S)-isopropyl 2-((chloro(phenoxy)phosphorothioyl)amino)propanoate (389 mg, 1.2 mmol). The reaction mixture was heated to 70° C. and stirred for 1 hour. The solvents were evaporated, and the resulting residue was purified by RP HPLC (MeCN and 0.1% HCOOH in water) to give compound 2a as a white solid (a mixture of 2 P-isomers, 100 mg, 44%). ¹H NMR (MeOD, 400 MHz) δ 7.81, 7.74 (2d, J=8.0 Hz, 1H), 7.16-7.36 (m, 5H), 5.94, 5.97 (2s, 1H), 5.61-5.69 (m, 1H), 5.54-5.58 (m, 1H), 5.42-5.47 (m, 1H), 5.24-5.39 (m, 1H), 4.86-4.99 (m, 1H), 4.50-4.55 (m, 1H), 4.34-4.42 (m, 1H), 4.17-4.21 (m, 2H), 4.02-4.12 (m, 1H), 1.31-1.38 (m, 3H), 1.21-1.23 (m, 6H). ³¹P NMR (CD₃OD, 162 MHz) δ 68.43, 68.10. ESI-LCMS: m/z 556.0 [M+H]⁺.

Example 3 Compound 3a

Step 1: Compound P3-1

Compound P2-2 (100 mg, 0.37 mmol) was dissolved in 20 mL of MeOH, and Pd/C (20 mg) was added. The resulting mixture was stirred at room temperature under H₂ (balloon) overnight. The reaction mixture was concentrated to give a residue. The resulting residue was purified by silica gel column chromatography (5% MeOH in DCM) to give P3-1 as white solid (90 mg, 94%). ¹H NMR (MeOD, 400 MHz) δ 7.97 (d, J=8.0 Hz, 1H), 6.01 (s, 1H), 5.69 (d, J=8.0 Hz, 1H), 3.92-3.97 (m, 2H), 3.86-3.89 (m, 1H), 3.76 (dd, J₁=2.8 Hz, J₂=12.4 Hz, 1H), 1.43-1.54 (m, 2H), 0.95 (t, J=7.6 Hz, 3H). ESI-MS: m/z 273 [M+H]⁺.

Step 2: Compound 3a

Compound P3-1 (90 mg, 0.33 mmol) was suspended in 2 mL of dry THF, followed by addition of NMI (0.6 mL) and (2S)-isopropyl 2-((chloro(phenoxy)phosphorothioyl)amino)propanoate (318 mg, 1.00 mmol). The reaction mixture was stirred at 70° C. for 1 hour. The solvents were evaporated, and the resulting residue was purified by RP HPLC (MeCN and 0.1% HCOOH in water) to give compound 3a as a white solid (a mixture of two P-isomers, 51 mg, 31%). ¹H NMR (MeOD, 400 MHz) δ 7.69, 7.63 (2d, J=8.0 Hz, 1H), 7.15-7.35 (m, 5H), 6.00, 6.04 (2s, 1H), 5.59, 5.58 (2d, J=8.0 Hz, 1H), 4.95-4.98 (m, 1H), 4.45-4.50 (m, 1H), 4.25-4.40 (m, 1H), 4.03-4.11 (m, 2H), 3.94, 3.93 (2d, J=9.2 Hz, 1H), 1.41-1.50 (m, 2H), 1.35, 1.31 (2d, J=16.8 Hz, 3H), 1.21, 1.22 (2d, J=6.0 Hz, 6H), 0.92-0.96 (m, 3H). ³¹P NMR (CD₃OD, 162 MHz) δ 68.35, 67.99. ESI-LCMS: m/z 558.0 [M+H]⁺.

Example 4 Preparation of additional 2′-C-ethynyluridine 5′-thiophosphoramidates

Compounds 7a-13a, 19a, and 21a as shown in Table 2, were prepared using a similar procedure for preparing compound 1a.

TABLE 2 ³¹P NMR ESI-LCMS Compound # Structure ppm m/z  7a

68.92 68.82 614.1 (M + 1)⁺  8a

70.44 69.26 582.1 (M + 1)⁺  9a

69.25 68.65 596.1 (M + 1)⁺ 10a

69.33 69.09 672.0 (M + 1)⁺ 11a

68.94 68.62 589.0 (M + 1)⁺ 12a

69.69 69.28 606.0 (M + 1)⁺ 13a

68.74 67.82 604.1 (M + 1)⁺ 19a

69.23 68.52 582.0 (M + 1)⁺ 21a

69.19 68.52 568.1 (M + 1)⁺

Example 5 Compound 5a

Step 1: Compound P5-1

To a stirred solution of P1-2 (2.0 g, 4.3 mmol) in THF (20 mL) was added 1-propynyl magnesium bromide (17.2 mL, 8.6 mmol) dropwise at −78° C. The resulting mixture was stirred at −78° C. for 2 hours. The reaction was quenched by addition of saturated aqueous NH₄Cl (50 mL). The solvent was removed in vacuo, and the resulting residue was diluted with ethyl acetate, washed with brine (100 mL), dried with Na₂SO₄, filtered, and concentrated to give a crude intermediate as a white solid (2.1 g, yield: 95%). The crude intermediate (2.1 g, 4.2 mmol) was dissolved in anhydrous DCM (150 mL), followed by addition of DMAP (1.0 g, 8.4 mmol), Et₃N (1.3 g, 12.6 mmol) and benzoyl chloride (1.76 g 12.6 mmol) at 0° C. The reaction mixture was stirred at room temperature overnight. The reaction mixture was diluted with DCM (100 mL), and washed with saturated aqueous NaHCO₃ (100 mL) and brine (100 mL). The organic phase was dried with Na₂SO₄, filtered, and evaporated to dryness under reduced pressure. The resulting residue was purified by silica gel column chromatography (0-20% petroleum ether in ethyl acetate) to give P5-1 as a yellow solid (1.2 g, yield: 48%).

Step 2: Compound P5-2

To a suspension of uracil (571 mg, 5.1 mmol) in 20 mL of acetonitrile was added N,O-bis(trimethylsilyl) acetamide (1.38 g, 6.8 mmol). The resultant solution was refluxed for 2 hours, and then cooled to ambient temperature. A solution of P5-1 (1.0 g, 1.7 mmol) in 20 mL of acetonitrile was added, followed by slow dropwise addition of SnCl₄ (1.76 g, 6.8 mmol). The reaction mixture was refluxed overnight, and then cooled to ambient temperature. Ethyl acetate (200 mL) was added, and the solution was washed with saturated NaHCO₃ and brine. The organic layer was dried with Na₂SO₄, filtered, and concentrated. The resulting residue was purified by silica gel column chromatography (30% petroleum ether in ethyl acetate) to afford the protected nucleoside as a white solid (412 mg, 42%). The protected intermediate (412 mg, 0.69 mmol) was dissolved in methanolic ammonia (100 mL, saturated) and the mixture was stirred at room temperature overnight. The solvent was removed, and the resulting residue was purified by column chromatography (3-˜8% MeOH in DCM) to give compound P5-2 as a white solid (171 mg, 87%). ¹H NMR (MeOD, 400 MHz) δ 8.10 (d, J=8.0 Hz, 1H), 6.03 (s, 1H), 5.72 (d, J=8.0 Hz, 1H), 3.99-4.06 (m, 2H), 3.91-3.94 (m, 1H), 3.82 (dd, J=2.8 Hz, J₂=12.4 Hz, 1H), 0.71-0.75 (m, 1H), 0.53-0.57 (m, 2H), 0.27-0.42 (m, 2H). ESI-TOF-MS: m/z 307 [M+Na]⁺.

Step 3: Compound 5a

To a stirred solution of P5-2 (110 mg, 0.38 mmol) and NMI (1 mL) in anhydrous acetonitrile (2 mL) was added a solution of (2S)-isopropyl 2-((chloro(phenoxy)phosphorothioyl)amino)propanoate (164 mg, 0.51 mmol) in 0.1 mL acetonitrile dropwise at room temperature under N₂. The mixture was stirred at 75° C. for 2 hours. The reaction was quenched with H₂O, and extracted ethyl acetate. The organic layer was dried over Na₂SO₄ and concentrated. The resulting residue was purified by RP HPLC (MeCN and 0.1% HCOOH in water) to give compound 5a as a white solid (a mixture of two P-isomers, 41 mg, 18.6%). ¹H NMR (MeOD, 400 MHz) δ 7.81, 7.74 (2d, J=8.0 Hz, 1H), 7.18-7.38 (m, 5H), 6.01, 6.04 (2s, 1H), 5.61 (d, J=8.0 Hz, 1H), 4.97-5.03 (m, 1H), 4.48-4.54 (m, 1H), 4.39-4.43 (m, 1H), 4.03-4.16 (m, 2H), 3.94-3.98 (m, 1H), 1.34-1.40 (m, 3H), 1.24-1.26 (m, 6H). ³¹P NMR (CD₃OD, 162 MHz) δ 68.39, 68.04. ESI-MS: m/z 570.0 [M+H]⁺.

Example 6 Compound 14a

Step 1: Compound P14-1

To a solution of P1-2 (7.6 g, 16.5 mmol) in THF (100 mL) was added 1-propynyl magnesium bromide (105.6 mL, 52.8 mmol) dropwise over 10 minutes at −78° C. The reaction mixture was stirred for 2 hours at −78° C. The reaction was quenched by the addition of saturated aqueous NH₄Cl (100 mL). The THF was removed in vacuo, and the resulting residue was diluted with ethyl acetate. The ethyl acetate layer was washed with brine (150 mL), dried with Na₂SO₄, filtered, and concentrated to give a crude intermediate as a white solid (7.6 g, 92%). The crude intermediate (7.6 g, 15.2 mmol) was dissolved in anhydrous DCM (150 mL), followed by addition of DMAP (3.8 g, 31.1 mmol), benzoyl chloride (7.0 mL, 45.6 mmol) and Et₃N (7.6 mL, 45.6 mmol) at 0° C. The reaction mixture was stirred at room temperature overnight. The reaction mixture was diluted with DCM (100 mL), and washed with saturated aqueous NaHCO₃ (150 mL) and brine (150 mL). The organic phase was dried with Na₂SO₄, filtered, and evaporated to dryness under reduced pressure. The resulting residue was purified by silica gel column chromatography (5% ethyl acetate in petroleum ether) to give P14-1 as a yellow solid (8.0 g, 87%).

Step 2: Compound P14-2

To a suspension of uracil (612 mg, 5.5 mmol) in 20 mL of distilled acetonitrile was added N,O-bis(trimethylsilyl) acetamide (1.486 g, 7.3 mmol). The solution was refluxed for 2 hours. The solution was cooled to ambient temperature. A solution of P14-1 (1.1 g, 1.8 mmol) in 20 mL of acetonitrile was added, followed by slow dropwise addition of SnCl₄ (1.89 g, 7.3 mmol). The reaction mixture was refluxed overnight. The solution was cooled to ambient temperature, and 200 mL of ethyl acetate was added. The solution was washed with saturated NaHCO₃ and brine. The organic layer was dried with Na₂SO₄, filtered, and concentrated to give a residue. The residue was purified by silica gel column chromatography (petroleum ether: ethyl acetate=100:1 to 3:1) to give the protected intermediate as a brown solid (150 mg, yield 14%). The protected intermediate (500 mg, 0.84 mmol) was dissolved in methanolic ammonia (100 mL, saturated) and the mixture was stirred overnight at room temperature. The solvent was removed, and the resulting residue was purified by column chromatography (DCM/MeOH=30:1 to 10:1) to give P14-2 as a white solid (155 mg, 65%). ¹H NMR (CD₃OD, 400 MHz) δ 8.02 (d, J=8.4 Hz, 1H), 6.00 (s, 1H), 5.68 (d, J=8.4 Hz, 1H), 4.1 (d, J=8.8 Hz, 1H), 3.94 (dd, J₁=2.0 Hz, J₂=12.4 Hz, 1H), 3.86-3.89 (m, 1H), 3.75 (dd, J₁=2.8, J₂=12.4 Hz, 1H), 1.75 (s, 3H). ESI-TOF-MS: m/z 305 [M+Na]⁺.

Step 3: Compound 14a

Compound P14-2 (105 mg, 0.37 mmol) was coevaporated with anhydrous pyridine and toluene three times, and then suspended in distilled acetonitrile (1 mL). NMI (0.5 mL) and a solution of (2S)-isopropyl 2-((chloro(phenoxy)phosphorothioyl)amino)propanoate in distilled acetonitrile (1M, 1 mL, 1.0 mmol) were added to the mixture. The reaction mixture was stirred at room temperature overnight. The solvents were evaporated, and the resulting residue was purified by HPLC (MeCN and 0.1% HCOOH in water) to give compound 14a as white solid (a mixture of two P-isomers, 41 mg, 20%). ¹H NMR (CD₃OD, 400 MHz) δ 7.76, 7.71 (2d, J=8.4 Hz, 1H), 7.15-7.35 (m, 5H), 6.04, 6.01 (2s, 1H), 5.59, 5.57 (2d, J=8.4 Hz, 1H), 4.95-5.01 (m, 1H), 4.44-4.49 (m, 1H), 4.26-4.39 (m, 1H), 4.02-4.13 (m, 3H), 1.76, 1.75 (2s, 3H), 1.36, 1.32 (2d, J=7.2 Hz, 3H), 1.24, 1.22 (2d, J=4.0 Hz, 6H). ³¹P NMR (CD₃OD, 162 MHz) δ 68.42, 68.30. ESI-LCMS: m/z 568 [M+H]⁺, 590 [M+Na]⁺.

Example 7 Compound 15a

Step 1: Compound P15-1

To a solution of P1-2 (39.0 g, 84.9 mmol) in anhydrous THF (450 mL) was added ethynylmagnesium bromide (390 mL, 195 mmol) dropwise over 20 minutes at −78° C. by cooling with an ice-acetone bath. The resulting mixture was stirred for 2 hours at −78° C. The ice-acetone bath was removed. Saturated NH₄Cl (600 mL) was added to the solution with stirring, and allowed to warm to room temperature. The mixture was filtered through CELITE™ and washed with saturated aqueous NH₄Cl (300 mL). The combined organic phase was dried with Na₂SO₄, filtered, and concentrated to provide a crude product (38.0 g). The crude product was dissolved in anhydrous DCM (200 mL), followed by addition of DMAP (19.1 g, 156.4 mmol), benzoyl chloride (23.5 g, 156.4 mmol) and Et₃N (23.7 g, 234.6 mmol). The reaction was stirred for 12 hours at room temperature. The reaction mixture was diluted with DCM (100 mL) and washed with saturated aqueous NaHCO₃ (100 mL). The combined aqueous phase was extracted with DCM (100 mL), and dried with Na₂SO₄, filtered and evaporated to dryness under reduced pressure. The resulting yellow oil was purified by column chromatography (5% ethyl acetate in petroleum ether) to P15-1 (18.0 g, yield: 39%).

Step 2: Compound P15-2

To a suspension of uracil (4.6 g, 40.6 mmol) in 20 mL of distilled acetonitrile was added N,O-bis(trimethylsilyl) acetamide (16.6 g, 81.3 mmol). The resultant solution refluxed for 30 minutes, and then cooled to ambient temperature. A solution of P15-1 (12.0 g, 20.34 mmol) in 10 mL of acetonitrile was added, followed by dropwise addition of SnCl₄ (21.15 g, 81.3 mmol). The reaction mixture was refluxed overnight, and then cooled to room temperature. The reaction mixture was diluted with 100 mL of ethyl acetate, and washed with saturated NaHCO₃ and brine. The organic layer was dried with Na₂SO₄, filtered, and concentrated. The resulting residue was purified via silica gel column chromatography (ethyl acetate/hexanes 5:1) to provide the protected nucleoside (7.6 g, yield 64%) as a white solid. The protected nucleoside was dissolved in methanolic ammonia (70 mL, saturated) and the mixture was stirred at room temperature for 14 hours. The solvent was removed, and the resulting residue was purified via silica gel column chromatography (DCM/MeOH=30:1 to 10:1) to provide P15-2 as a white solid (1.9 g, 56%). ¹H NMR (CD₃OD, 400 MHz) δ 8.05 (d, J=8.0 Hz, 1H), 6.02 (s, 1H), 5.68 (d, J=8.0 Hz, 1H), 4.19 (d, J=8.8 Hz, 1H), 3.93 (dd, J₁=2.4 Hz, J₂=12.4 Hz, 1H), 3.88-3.92 (m, 1H), 3.76 (dd, J₁=2.8 Hz, J₂=12.8 Hz, 1H), 3.02 (s, 1H); EST-TOF-MS: m/z 291 [M+Na]⁺.

Step 3: Compound P15-3

A solution of P15-2 (200 mg, 074 mmol) in acetone was treated at room temperature with N-iodosuccinimide (NIS) (200 mg, 0.8 mmol) and silver nitrate (61 mg, 3.7 mmol). After 1 hour the reaction mixture was poured with stirring into ice water. The resulting precipitate was filtered and dissolved in ethyl acetate. The resulting solution was washed with water, dried, and evaporated to dryness in vacuo. The resulting residue was purified by column chromatography (DCM/MeOH=20:1) to give P15-3 (115 mg, 52%). ¹H NMR (CD₃OD, 400 MHz) δ 8.00 (d, J=8.0 Hz, 1H), 6.0 (s, 1H), 5.70 (d, J=8.0 Hz, 1H), 4.15 (d, J=9.2 Hz, 1H), 3.85-3.96 (m, 2H), 3.74 (dd, J₁=2.8 Hz, J₂=12.4 Hz, 1H); ESI-TOF-MS: m/z 395 [M+H]⁺.

Step 4: Compound 15a

Compound P15-3 (100 mg, 0.25 mmol) was suspended in 2 ml of dry MeCN, followed by addition of NMI (1 mL) and (2S)-isopropyl 2-((chloro(phenoxy)phosphorothioyl)amino)propanoate (243 mg, 0.75 mmol). The reaction mixture was stirred for 12 hours. The solvents were evaporated, and the resulting residue was purified by RP HPLC (MeCN and 0.1% HCOOH in water) to give compound 15a (a mixture of two P isomers, 62 mg, 38%). ¹H NMR (CD₃OD, 400 MHz) δ 7.73, 7.67 (2d, J=8.0 Hz, 1H), 7.18-7.36 (m, 5H), 6.03, 6.00 (2s, 1H), 5.62, 5.57 (2d, J=8.0 Hz, 1H), 4.95-5.01 (m, 1H), 4.44-4.50 (m, 1H), 4.25-4.37 (m, 1H), 4.05-4.17 (m, 3H), 1.32-1.37 (m, 3H), 1.22-1.24 (m, 3H); ³¹P NMR (CD₃OD, 162 MHz) 668.4, 68.2; ESI-LCMS: m/z 680 [M+H]⁺.

Example 8 Compound 16a

Step 1: Compound P16-2

To an ice-cold solution of P16-1 (2.0 g, 7.6 mmol) in anhydrous pyridine (20 mL) was added 1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane (2.40 g, 7.6 mmol) under N₂. The reaction mixture was stirred at room temperature overnight. The solvent was removed under vacuum. The resulting residue was diluted with ethyl acetate (100 mL), and washed with saturated NaHCO₃ and brine. The organic layer was separated, dried over anhydrous Na₂SO₄, and filtered. The filtrate was concentrated in vacuo to give a residue. The residue was purified by silica gel column chromatography (DCM/MeOH=100/1 to 50/1) to give P16-2 as a white solid (3.2 g, 85%).

Step 2: Compound P16-3

Pyridine (4.5 ml) and acetic anhydride (3.2 mL) were added to a suspension of CrO₃ (3.2 g, 32 mmol) in DCM (80 mL) under N₂ at 0° C. The mixture was stirred at room temperature for 30 minutes before a solution of P16-2 (3.2 g, 6.6 mmol) in DCM (20 mL) was added at 0° C. The mixture was stirred at room temperature for 1 hour. The mixture was filtered through a silica gel pad, and the filtrate was evaporated to dryness to give a ketone intermediate as a white solid (2.8 g, 90%).

Separately, trimethylsilylacetylene (2.0 g, 20 mmol) was dissolved in anhydrous THF (40 mL), and n-BuLi (8.0 mL, 20 mmol) was added dropwise at −78° C. The reaction mixture was stirred at −78° C. for 30 minutes. The reaction mixture was warmed to room temperature for 10 minutes.

Then, the ketone intermediate (2.0 g, 4.0 mmol) in THF (10 mL) was added to the reaction mixture dropwise at −78° C. The reaction mixture was stirred at −78° C. for 1 hour, warmed to room temperature, and stirred for an additional 20 minutes. The reaction was quenched by saturated NH₄Cl at −78° C. The reaction was diluted with ethyl acetate, washed with brine, dried by Na₂SO₄, and concentrated to give a residue. The residue was purified by silica gel column chromatography (15% ethyl acetate in petroleum ether) to give P16-3 as a white solid (920 mg, 46%).

Step 3: Compound P16-4

Compound P16-3 (900 mg, 1.54 mmol) was dissolved in anhydrous toluene (10 mL) under argon and cooled to −78° C. in an cooling bath. Diethylaminosulfur trifluoride (DAST) (1.5 g, 9.0 mmol) was added dropwise, and the cooling bath was removed. Stirring was continued for 1.5 hours. The mixture was diluted with ethyl acetate and poured into saturated NaHCO₃. The organic layer was separated, washed with brine, dried by Na₂SO₄, and concentrated to give a residue. The residue was purified by silica gel chromatography (20% ethyl acetate in petroleum ether) to give P16-4 as a white solid (720 mg, 79%).

Step 4: Compound P16-5

A mixture of P16-4 (700 mg, 1.0 mmol) and NH₄F (800 mg, 21.6 mmol) in methanol (10 mL) was refluxed for 2 hours. After cooling to room temperature, the mixture was concentrated to dryness. The resulting residue was purified by silica gel column chromatography (5-˜8% MeOH in DCM) to give P16-5 as a white solid (240 mg, 58%). ¹H NMR (DMSO-d6, 400 MHz) δ 9.55 (bs, 2H), 7.62 (s, 1H), 5.82 (d, J=7.6 Hz, 1H), 5.00 (s, 1H), 4.94 (s, 1H), 4.06-4.12 (m, 1H), 3.82 (d, J=5.2 Hz, 1H), 3.72-3.75 (m, 1H), 3.66-3.68 (m, 1H), 3.51-3.55 (m, 1H). ESI-TOF-MS: m/z 293 [M+Na]⁺.

Step 5: Compound 16a

Compound P16-5 (150 mg, 0.56 mmol) was suspended in 2 mL of dry MeCN, and NMI (1 mL) and (2S)-isopropyl 2-((chloro(phenoxy)phosphorothioyl)amino)propanoate (536 mg, 1.68 mmol) were added. The reaction mixture was stirred for 12 hours. The solvent was evaporated, and the resulting residue was purified by HPLC (MeCN and 0.1% HCOOH in water) to give compound 16a as a white solid (a mixture of 2 P-isomers, 82 mg, 26%). ¹H NMR (MeOD, 400 MHz) δ 7.70, 7.62 (2d, J=8.0 Hz, 1H), 7.17-7.36 (m, 5H), 6.25, 6.22 (2d, J=18.0 Hz, 1H), 5.65, 5.57 (2d, J=8.0 Hz, 1H), 4.94-4.99 (m, 1H), 4.49-4.56 (m, 1H), 4.22-4.41 (m, 2H), 4.01-4.17 (m, 2H), 3.54, 3.52 (2d, J=5.2 Hz, 1H), 1.36, 1.33 (2d, J=6.8 Hz, 3H), 1.23, 1.22 (2d, J=6.4 Hz, 6H). ³¹P NMR (CD₃OD, 162 MHz) δ 68.51, 68.43. ESI-LCMS: m/z 578.0 [M+Na]⁺.

Example 9 Compound 18a

Step 1: Compound P18-1

To a stirred solution of but-1-yne (2.9 g, 0.35 mol) in anhydrous THF (40 mL) was added n-BuLi (20 mL, 0.05 mol) dropwise at −78° C. The reaction mixture was stirred for 30 minutes at −78° C., and then allowed to warm to room temperature. A solution of P1-2 (5.0 g, 0.01 mol) in THF was added dropwise at −78° C. The reaction mixture was stirred for 1 hour at −78° C., and then quenched by careful addition of aqueous saturated NH₄Cl. The mixture was warmed to room temperature. The mixture was diluted with ethyl acetate, washed with saturated brine, dried by NaSO₄, and concentrated to dryness. The resulting residue was purified by column chromatography to provide a crude product. The crude product was dissolved in anhydrous DCM (50 mL), followed by addition of DMAP (2.5 g, 19.4 mmol), benzoyl chloride (4.0 g, 29.2 mmol) and Et₃N (3.0 g, 29.2 mmol). The reaction was stirred at room temperature for 12 hours. The reaction mixture was diluted with DCM (50 mL), and washed with saturated aqueous NaHCO₃ (50 mL). The combined aqueous phase was extracted with DCM (100 mL). The combined organic phase was dried with Na₂SO₄, filtered, and evaporated to dryness under reduced pressure to give a yellow oil. The oil was purified by column chromatography (5% ethyl acetate in petroleum ether) to give P18-1 (3.8 g, yield: 40%).

Step 2: Compound P18-2

To a suspension of uracil (1.9 g, 16 mmol) in 10 mL of distilled acetonitrile was added N,O-bis(trimethylsilyl) acetamide (6.9 g, 33 mmol). The resultant solution was refluxed for 30 minutes. The solution was then cooled to ambient temperature. A solution of P18-1 (3.5 g, 5.6 mmol) in 10 mL of acetonitrile was added, followed by addition of SnCl₄ (8.0 g, 33 mmol). The reaction mixture was refluxed overnight. The reaction mixture was cooled to room temperature, diluted with 100 mL of ethyl acetate, and washed with saturated NaHCO₃ and brine. The organic layer was dried with Na₂SO₄, filtered, and concentrated. The resulting residue was purified by silica gel column chromatography (ethyl acetate/hexanes 4:1) to afford the protected nucleoside intermediate (2.6 g, 80%) as a white solid. The intermediate was dissolved in methanolic ammonia (50 mL, saturated). The mixture was stirred at room temperature for 14 hours. The solvent was removed, and the resulting residue was purified by column chromatography (DCM/MeOH=30:1 to 10:1) to give P18-2 as a white solid (850 mg, 67%). ¹H NMR (CD₃OD, 400 MHz) δ 8.03 (d, J=8.0 Hz, 1H), 6.01 (s, 1H), 5.68 (d, J=8.0 Hz, 1H), 4.10 (d, J=8.8 Hz, 1H), 3.47 (dd, =2.4 Hz, J₂=12.4 Hz, 1H), 3.88 (ddd, ==2.8 Hz, J₃=8.8 Hz, 1H), 3.75 (dd, J₁=2.8 Hz, J₂=12.8 Hz, 1H), 2.14 (q, J=7.6 Hz, 2H), 1.02 (t, J=7.6 Hz, 3H); ESI-TOF-MS: m/z 319 [M+Na]⁺.

Step 3: Compound 18a

Compound P18-2 (150 mg, 0.5 mmol) was suspended in 1.5 mL of dry MeCN. NMI (0.5 mL) and (2S)-isopropyl 2-((chloro(phenoxy)phosphorothioyl)amino)propanoate (478 mg, 1.5 mmol) were added. The reaction mixture was stirred for 12 hours. The solvents were evaporated, and the resulting residue was purified by RP HPLC (MeCN and 0.1% HCOOH in water) to give compound 18a (a mixture of two P isomers, 78 mg, 27%). ¹H NMR (CD₃OD, 400 MHz) δ 7.77, 7.72 (2d, J=8.0 Hz, 1H), 7.15-7.36 (m, 5H), 6.04, 6.02 (2s, 1H), 5.58, 5.57 (2d, J=8.0 Hz, 1H), 4.95-5.01 (m, 1H), 4.45-4.51 (m, 1H), 4.27-4.39 (m, 1H), 4.06-4.12 (m, 3H), 2.10-2.18 (m, 2H), 1.36, 1.32 (2d, J=7.6 Hz, 3H), 1.20-1.26 (m, 6H), 0.99-1.04 (m, 3H); ³¹P NMR (CD₃OD, 162 MHz) δ 68.45, 68.22; ESI-LCMS: m/z 604 [M+Na]⁺582 [M+H]⁺.

Example 10 Compound 20a

Step 1: Compound P20-1

To a solution of 3-methyl-1-butyne (3.7 g, 0.05 mol) in anhydrous THF (40 mL) was added n-BuLi (13 mL, 0.03 mol) dropwise at −78° C. The reaction mixture was stirred for 30 minutes at −78° C. A solution of P1-2 (4.8 g, 0.01 mol) in THF was added dropwise at −78° C. The reaction mixture was stirred for 1 hour at −78° C. and then quenched by addition of aqueous NH₄Cl at −78° C. The mixture was warmed to room temperature. The mixture was diluted with ethyl acetate, washed with saturated brine, dried by NaSO₄, and concentrated to dryness. The resulting residue was purified via silica gel column chromatography to give a crude product. The crude product was dissolved in anhydrous DCM (50 mL), followed by addition of DMAP (2.6 g, 21.6 mmol), benzoyl chloride (4.0 g, 30 mmol) and Et₃N (3.3 g, 32.4 mmol). The reaction mixture was stirred for 12 hours at room temperature. The reaction mixture was diluted with DCM (50 mL), and washed with saturated aqueous NaHCO₃ (50 mL). The combined aqueous phase was extracted with DCM (100 mL). The combined organic phase was dried with Na₂SO₄, filtered, and evaporated to dryness under reduced pressure to give a yellow oil. The oil was purified by column chromatography (5% ethyl acetate in petroleum ether) to give P20-1 (3.1 g, 43%) as white foam.

Step 2: Compound P20-2

To a suspension of uracil (800 mg, 6.5 mmol) in 10 mL of MeCN was added N,O-bis(trimethylsilyl) acetamide (3.0 g, 15 mmol). The mixture was refluxed for 30 minutes, and then cooled to room temperature. A solution of P20-1 (2.5 g, 3.3 mmol) in acetonitrile (10 mL) was added, followed by addition of SnCl₄ (3.5 g, 15 mmol). The reaction mixture was refluxed overnight. The reaction mixture was cooled to room temperature. The reaction mixture was diluted with 100 mL of ethyl acetate, and washed with saturated NaHCO₃ and brine. The organic layer was dried with Na₂SO₄, filtered, and concentrated. The resulting residue, was purified by silica gel column chromatography (ethyl acetate/hexanes 5:1) to afford the protected nucleoside intermediate (1.4 g, 64%) as a white solid. The protected intermediate was treated with methanolic ammonia (saturated) at room temperature for 14 hours. The solvent was removed, and the resulting residue was purified by column chromatography (DCM/MeOH=30:1 to 10:1) to give P20-2 as a white solid (510 mg, 74%). ¹H NMR (DMSO-d6, 400 MHz) δ 11.34 (br s, 1H), 7.92 (d, J=8.0 Hz, 1H), 6.01 (s, 1H), 5.94 (s, 1H), 5.87 (s, 1H), 5.63 (d, J=8.0 Hz, 1H), 5.53 (d, J=7.6 Hz, 1H), 5.18 (t, J=7.2 Hz, 1H), 3.95 (dd, J=J_(z)=8.8 Hz, 1H), 3.73-3.79 (m, 2H), 3.56-3.60 (m, 1H), 2.46 (q, J=7.2 Hz, 1H), 0.98 (t, J=7.2 Hz, 6H); Negative-ESI-TOF-MS: m/z 309 [M−H]⁺.

Step 3: Compound 20a

To a suspension of P20-2 (80 mg, 0.25 mmol) in MeCN (1.5 mL) were added NMI (0.5 mL) and (2S)-isopropyl 2-((chloro(phenoxy)phosphorothioyl)amino)propanoate (308 mg, 0.7 mmol). The reaction mixture was stirred at room temperature for 12 hours. The solvents were evaporated, and the resulting residue was purified by RP HPLC (MeCN and 0.1% HCOOH in water) to provide compound 20a (a mixture of two P isomers, 32 mg, 21%). ¹H NMR (CD₃OD, 400 MHz) δ 7.77, 7.72 (2d, J=8.0 Hz, 1H), 7.15-7.36 (m, 5H), 6.04, 6.01 (2s, 1H), 5.58, 5.57 (2d, J=8.0 Hz, 1H), 4.95-5.01 (m, 1H), 4.45-4.51 (m, 1H), 4.27-4.39 (m, 1H), 4.08-4.12 (m, 3H), 2.47-2.54 (m, 2H), 1.31-1.37 (m, 3H), 1.23, 1.22 (2d, J=6.4 Hz, 6H), 1.04-1.08 (m, 6H); ³¹P NMR (CD₃OD, 162 MHz) δ 68.515, 68.13; ESI-LCMS: m/z 618 [M+Na]⁺.

Example 11 Compound 22a

Step 1: Compound P22-2

To a solution of P22-1 (obtained as in Org. Lett., 2007, 9, 3009-3012, which is hereby incorporated by reference for the purpose of synthesizing P22-1) in dry THF (400 mL) under an argon atmosphere at −78° C., allylmagnesium bromide (400 mL, 400 mmol; 1.0 M in diethylether) is added. After stirring the reaction mixture at −78° C. for 4 hours, the reaction mixture is allowed to stir at room temperature for 2 hours. The reaction is carefully quenched with saturated aqueous ammonium chloride. The mixture is extracted with dichloromethane, and the organic layer is washed with brine. The solvent is removed, and the residue is purified by silica gel chromatography, by gradient elution with 15% to 20% ethyl acetate in hexane to give P22-2 as a colorless oil.

Step 2: Compound P22-3

To a solution of P22-2 (26.6 g, 69.2 mmol) in dry dichloromethane (500 mL) at room temperature, DMAP (2.113 g, 17.30 mmol), triethylamine (217 mL, 1557 mmol) and benzoyl chloride (18.05 mL, 156 mmol) are added. After 1 hour, additional benzoyl chloride (6 mL) and DMAP (2.1 g) are added. The mixture is stirred for 5 days. The reaction mixture is then stirred with 1 N HCl and extracted with dichloromethane. The organic layers are combined and washed with saturated aqueous NaHCO₃ followed by brine. After drying with MgSO₄, filtration and evaporation of the volatiles, the residue is purified by column chromatography (400 g silica) eluting with heptane to 15% ethyl acetate in heptane to give P22-3 as an oil (as a mixture with P22-2). The mixture is purified again with DCM as eluent. The pure fractions are collected and P22-3 is obtained as a colorless oil.

Step 3: Compound P22-4

Bis(trimethylsilyl)acetamide (BSA; 29.2 mL, 118 mmol) is added to a mixture of P22-3 (14.0 g, 23.1 mmol) and uracil (5.99 g, 53.4 mmol) in anhydrous acetonitrile (300 mL). The reaction mixture is refluxed for 1 hour and the solution is allowed to cool to room temperature. Tin chloride (11.55 mL, 99 mmol) is added dropwise at room temperature and the mixture is further stirred for 1 hour. The mixture is then stirred at reflux for 1.5 hour and again cooled to room temperature. Ethyl acetate (250 mL) is added, followed by saturated aqueous NaHCO₃ (250 mL) and the mixture is stirred for 15 minutes. After filtration through CELITE™, the organic layer is separated and washed with saturated aqueous NaHCO₃ (250 mL). The combined aqueous layer is extracted with ethyl acetate (250 mL) and the combined organic layer is dried (MgSO₄), filtered and evaporated to dryness under reduced pressure. The resulting yellow oil is dissolved in methanol and 25% sodium methanolate (25 mL) is added. Stirring is continued overnight. Then 25% sodium methanolate (15 mL) is added and stirring is continued overnight. Acetic acid (30 mL) is added and the solvent is removed. The residue is purified by column chromatography with heptane/ethyl acetate 50:50 to 100% ethyl acetate. Compound P22-4 is obtained as a colorless oil.

Step 4: Compound P22-5

To a stirred solution of P22-4 (7.8 g, 16.79 mmol) in a mixture of THF (10 mL) and H₂O (10 mL) is added sodium periodate (11.17 g, 52.2 mmol) followed by osmium(VIII) tetroxide (2 mL, 2.5 w/v % in tert-butanol, 0.168 mmol) and stirring is continued for 2 hours at room temperature. Water (100 mL) is added and extraction is performed with ethyl acetate (2×50 mL). The organic layer is washed with saturated aqueous NaHCO₃ (2×30 mL). The combined aqueous layer is extracted with ethyl acetate and the combined organic layer is dried over (Na₂SO₄), filtered and evaporated to dryness under reduced pressure. The oily residue obtained is dissolved in a mixture of THF (100 mL) and H₂O (20 mL) and sodium borohydride (1.361 g, 36.0 mmol) is added. The reaction mixture is stirred overnight at room temperature, whereupon water (100 mL) is added and extraction is performed with ethyl acetate (2×50 mL). The combined organic layer is washed with saturated aqueous NaHCO₃, the combined aqueous layer is extracted with ethyl acetate, and the combined organic layer is dried over (Na₂SO₄), filtered and evaporated to dryness under reduced pressure. The oily residue obtained is purified by column chromatography (0-10% (v/v) methanol in DCM then 10% isocratic) affording P22-5 as a white foam.

Step 5: Compound P22-6

Methanesulfonyl chloride (0.800 mL, 10.34 mmol) is added to P22-5 (4.32 g, 9.22 mmol) in dry pyridine (100 mL). After 1 hour and 15 minutes, 0.1 equivalents more methanesulfonyl chloride is added and the mixture is further stirred at room temperature for 45 minutes. A small amount of methanol is added and the mixture is evaporated to dryness. The residue is dissolved in ethyl acetate (100 mL) and washed with saturated NaHCO₃ (2×50 mL). The combined aqueous layer is extracted with ethyl acetate. The combined organic layer is then dried over Na₂SO₄ and concentrated in vacuo. The obtained residue is dissolved in dry THF and 95% NaH (932 mg, 36.9 mmol) is added at once at room temperature. After stirring for 2 hours at room temperature, the reaction mixture is poured on a saturated aqueous solution NH₄Cl (30 mL) followed by addition of DCM (250 mL). The separated organic layer is washed with saturated aqueous NaHCO₃ (2×100 mL) and the combined aqueous layer is extracted with DCM (250 mL). The combined organic layer is dried (Na₂SO₄), filtered and evaporated to dryness under reduced pressure. The residue obtained is purified by column chromatography eluting first with heptane, then with ethyl acetate to provide P22-6 as a foam.

Step 6: Compound P22-7

A mixture of P22-6 (50 mg, 0.111 mmol) in methanol (1 mL) and Pd(OH)₂ (8 mg) is stirred under a hydrogen atmosphere at room temperature. After 4 hours, more Pd(OH)₂ (30 mg) and methanol (1 mL) are added. The mixture is stirred vigorously under H₂-atmosphere overnight. The catalyst is removed by filtration over decalite, and the solvent is removed by evaporation. The resulting residue is purified by silica gel chromatography eluted with 10% methanol in ethyl acetate to give P22-7 as a white powder.

Step 7: Compound 22a

To a suspension of P22-7 (0.25 mmol) in MeCN are added NMI (0.5 mL) and (2S)-isopropyl 2-((chloro(phenoxy)phosphorothioyl)amino)propanoate (0.7 mmol). The reaction mixture is stirred at room temperature for 12 hours. The solvents are evaporated, and the resulting residue is purified by RP HPLC to provide compound 22a.

Example 12 Compound 6a

Step 1: Compound 6-2

To a solution of Dess-Martin periodinane (12.0 g, 28.1 mmol) in 500 mL of CH₂Cl₂ was added 6-1 (8.0 g, 17.3 mmol) at 0° C. The mixture was warmed to R.T. and stirred for 12 h. The solvent was removed in vacuo. The residue was triturated with TBME (150 mL) and filtered through a pad of MgSO₄. The filtrate was stirred with an equal volume of Na₂S₂O₃.5H₂O in 50 mL of saturated NaHCO₃ until the organic layer became clear (10 min). The organic layer was separated, washed with brine, dried over MgSO₄ and concentrated to give 6-2 (7.3 g, 91%) as a white solid.

Step 2: Compound 6-3

To a solution of 6-2 (13.0 g, 28.3 mmol) in anhydrous THF (150 mL) was added ethynylmagnesium bromide (130 mL, 65 mmol) dropwise over 20 min at −78° C. The mixture stirred for 2 h at −78° C. The ice-acetone cooling bath was removed and saturated NH₄Cl (200 mL) was added with stirring. After warming to R.T., the mixture was filtered through celite and washed by saturated aq. NH₄Cl (100 mL). The combined organic phase was dried with Na₂SO₄, filtered and concentrated to give a crude product. This reaction starting with 6-2 was repeated 2 more times to give 38.0 g of the crude product. The crude product was dissolved in anhydrous CH₂Cl₂ (200 mL), whereupon DMAP (19.1 g, 156.4 mmol), benzoyl chloride (23.5 g, 156.4 mmol) and Et₃N (23.7 g, 234.6 mmol) were added. After stirring for 12 h at R.T., the mixture was diluted with CH₂Cl₂ (100 mL) and then washed with saturated aq. NaHCO₃ (100 mL). The combined aqueous phase was extracted with DCM (100 mL). The combined organic phase was dried with Na₂SO₄, filtered and evaporated to dryness under reduced pressure to give a yellow oil, which was purified by column chromatography (5% EA in PE) to give 6-3 (18.0 g, 39%) as a white solid.

Step 3: Compound 6-4

To a stirred suspension of 6-3 (2.0 g, 3.38 mmol) and 6-chloro-9H-purin-2-amine (1.2 g, 7.10 mmol) in anhydrous MeCN (20 mL) was added DBU (3.1 g, 20.39 mmol) at 0° C. The mixture was stirred at 0° C. for 5 mins and then TMSOTf (6.0 g, 24.0 mmol) was added dropwise at 0° C. After addition, the mixture was stirred at 0° C. for 20 mins until a clear solution was achieved. The mixture was heated to 70° C. and stirred for 3 h. The reaction was monitored by LCMS. The reaction was cooled R.T. and diluted with EA. The solution was washed with saturated NaHCO₃ and brine in sequence. The organic layer was dried over Na₂SO₄ and concentrated. The residue was purified on a silica gel column (20-25% EA in PE) to give 6-4 (1.1 g, 57%) as light yellow foam.

Step 4: Compound 6-5

To a mixture of 6-4 (1.0 g, 1.5 mmol), AgNO₃ (765 mg, 4.5 mmol) and collidine (10 mL) in anhydrous pyridine (20 mL) was added MMTrCl (1.5 g, 4.5 mmol) in small portions under N₂. The mixture was stirred at R.T. for 12 h under N₂. The reaction was allowed to continue until TLC showed the reaction was completed. The mixture was filtered, and the solvent was removed under vacuum. The residue was diluted with EA, and washed with water and brine. The organic layer was separated, dried over anhydrous Na₂SO₄ and concentrated to dryness. The residue was purified on a silica gel column (5-10% EA in PE) to give 6-5 (1.2 g, 86%) as a white solid.

Step 5: Compound 6-6

To a solution of 3-Hydroxy-propionitrile (3.7 g, 52 mmol) in THF (50 mL) was added NaH (624 mg, 26 mmol) at 0° C. The mixture was stirred at R.T. for 15 mins. To the mixture was added 6-5 (1.2 g, 1.3 mmol). The mixture was then stirred at R.T. for 12 h. The mixture was concentrated to give a residue which was purified by column chromatography (1-2% MeOH in DCM) to give 6-6 (480 mg, 48%). ¹H NMR (Methanol-d₄, 400 MHz) δ 8.04 (s, 1H), 7.18-7.34 (m, 12H), 6.84 (d, J=8.8 Hz, 2H), 5.35 (s, 1H), 4.32 (d, J=8.8 Hz, 1H), 3.82-3.89 (m, 2H), 3.76 (s, 3H), 3.67-3.71 (m, 1H), 2.61 (s, 1H).

Step 6: Compound 6a

To a mixture of 6-6 (136 mg, 0.22 mmol) and NMI (0.6 mL) in anhydrous MeCN (2 mL) was added thiophosphochloridate (224 mg, 0.70 mmol) at 0° C. The mixture was stirred at R.T. for 12 h. The mixture was then concentrated, and the residue was purified by column chromatography to give a crude protected intermediate (100 mg, 60.9%). The crude protected intermediate was dissolved in a 80% HCOOH aqueous solution (10 mL), and the mixture was stirred at R.T. for 12 h. The solvent was removed under vacuum, and the residue was purified on a silica gel column (2-5% MeOH in DCM) to give 6a (31 mg, 43.6%) as a white solid. ¹H NMR (DMSO-d₆, 400 MHz) δ 8.37 (s, 1H), 7.80 (d, J=3.6 Hz, 2H), 7.16-7.37 (m, 5H), 6.38-6.73 (m, 4H), 5.84-5.99 (m, 2H), 4.79-4.86 (m, 1H), 3.93-4.38 (m, 5H), 3.32 (s, 1H), 1.10-1.27 (m, 9H). ³¹P NMR (DMSO-d₆, 162 MHz) δ 68.20, 67.68. ESI-LCMS: m/z 593.0 [M+H]⁺.

Example 13 Compound 4a

Step 1: Compound 4-1

To a stirred suspension of 6-3 (2.0 g, 3.38 mmol) and 6-chloro-9H-purine (924 mg, 6.0 mmol) in anhydrous MeCN (20 mL) was added DBU (3.1 g, 20.2 mmol) at 0° C. The mixture was stirred at 0° C. for 5 minutes and then TMSOTf (6.0 g, 24.0 mmol) was added dropwise at 0° C. After addition, the mixture was stirred at 0° C. for 20 mins until a clear solution was achieved. The mixture was heated to 70° C. and stirred for 3 h. The reaction was monitored by LCMS. The reaction was cooled to R.T. and diluted with EA. The solution was washed with saturated NaHCO₃ and brine in sequence. The organic layer was dried over Na₂SO₄ and then concentrated. The residue was purified on a silica gel column (10-20% EA in PE) to give 4-1 (1.1 g, 52%) as a light yellow foam.

Step 2: Compound 4-2

To a solution of 4-1 (1.1 g, 1.7 mmol) in 1,4-dioxane (10 mL) was added aqueous ammonia (30 mL) at R.T. The mixture was stirred at 100° C. in a sealed vessel for 10 h. The mixture was cooled to R.T., and the solvent was removed under reduced pressure. The residue was purified on a silica gel column (5-10% MeOH in DCM) to give 4-2 (256 mg, 80%) as a white solid. ¹H NMR (DMSO-d₆, 400 MHz) δ 8.38 (s, 1H), 8.13 (s, 1H), 7.26 (s, 2H), 6.37 (s, 1H), 6.04 (s, 1H), 5.76 (d, J=7.2 Hz, 1H), 5.27 (t, J=5.2 Hz, 1H), 4.43-4.47 (m, 1H), 3.87-3.91 (m, 1H), 3.77-3.82 (m, 1H), 3.64-3.70 (m, 1H), 3.13 (s, 1H). ESI-MS: m/z 292.1 [M+H]⁺.

Step 3: Compound 4a

To a solution of 4-2 (150 mg, 0.52 mmol) and NMI (0.6 mL) in anhydrous MeCN (2 mL) was added thiophosphochloridate (496 mg, 1.54 mmol) at 0° C. The mixture was stirred at R.T. overnight. The solvent was then evaporated, and the residue was purified by HPLC separation (0.1% HCOOH in water and MeCN) to give 4a (68 mg, 23%). ¹H NMR (DMSO-d₆, 400 MHz) δ 8.38 (s, 1H), 8.21 (s, 1H), 8.14 (s, 1H), 7.16-7.37 (m, 5H), 6.49-6.66 (m, 2H), 6.07-6.09 (m, 1H), 5.97-6.03 (m, 1H), 4.71-4.86 (m, 1H), 4.59-4.60 (m, 1H), 4.21-4.38 (m, 1H), 4.10-4.17 (m, 1H), 3.90-3.93 (m, 1H), 3.21 (s, 1H), 1.04-1.24 (m, 9H). ³¹P NMR (DMSO-d₆, 162 MHz) δ 67.98, 67.95. ESI-MS: m/z 576.9 [M+H]⁺.

Example 14 Compound 17a

Step 1: Compound 17-1

6-6 (500 mg, 0.86 mmol) was dissolved in a 80% HCOOH solution (20 mL). The mixture was stirred at R.T. for 12 h. The solvent was removed under vacuum, and the residue was purified on a silica gel column (2-5% MeOH in DCM) to give as 17-1 (200 mg, 75.4%) as a white solid.

Step 2: Compound 17a

To a solution of 17-1 (350 mg, 1.14 mmol) and NMI (0.6 mL) in anhydrous CH₃CN (2 mL) was added thiophosphochloridate (649 mg, 1.8 mmol) at 0° C. The mixture was stirred at R.T. for 12 h. The solvent was then evaporated, and the residue was purified by HPLC separation (0.1% HCOOH in water and MeCN) to give 17a (90 mg, 24%) as a white solid. ¹H NMR (Methanol-d₄, 400 MHz) δ 7.90 (d, J=2.4 Hz, 1H), 7.24-7.33 (m, 4H), 7.13-7.17 (m, 1H), 6.01 (d, J=12.8 Hz, 1H), 4.61-4.71 (m, 1H), 4.34-4.51 (m, 3H), 4.03-4.21 (m, 2H), 2.80 (d, J=3.2 Hz, 1H), 1.67-1.79 (m, 4H), 1.23-1.50 (m, 9H). ³¹P NMR (Methanol-d₄, 162 MHz) δ 68.41, 68.36. ESI-MS: m/z 633.1 [M+H]⁺.

Example 15 HCV Replicon Assay Cells

Huh-7 cells containing the self-replicating, subgenomic HCV replicon with a stable luciferase (LUC) reporter were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 2 mM L-glutamine and supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% penicillin-streptomyocin, 1% nonessential amino acids, and 0.5 mg/mL G418.

Determination of Anti-HCV Activity

Determination of 50% inhibitory concentration (EC₅₀) of compounds in HCV replicon cells were performed by the following procedure. On the first day, 5,000 HCV replicon cells were plated per well in a 96-well plate. On the following day, test compounds were solubilized in 100% DMSO to 100× the desired final testing concentration. Each compound was then serially diluted (1:3) up to 9 different concentrations. Compounds in 100% DMSO are reduced to 10% DMSO by diluting 1:10 in cell culture media. The compounds were diluted to 10% DMSO with cell culture media, which were used to dose the HCV replicon cells in 96-well format. The final DMSO concentration was 1%. The HCV replicon cells were incubated at 37° C. for 72 hours. At 72 hours, cells were processed when the cells are still subconfluent. Compounds that reduce the LUC signal are determined by Bright-Glo Luciferase Assay (Promega, Madison, Wis.). % Inhibition was determined for each compound concentration in relation to the control cells (untreated HCV replicon) to calculate the EC₅₀.

Compounds of Formula (I) are active in the replicon assay. The antiviral activity of exemplary compounds is shown in Table 3, where ‘A’ indicates an EC₅₀<1 μM, ‘B’ indicates an EC₅₀≧1 μM and <10 μM, and ‘C’ indicates an EC₅₀≧10 μM and <100 μM.

TABLE 3 # Structure EC₅₀  1a

A  2a

B  4a

A  6a

B  7a

A  8a

C  9a

B 10a

A 11a

A 12a

A 13a

A 14a

B 15a

A 16a

B 17a

B 18a

C 19a

A 20a

C 21a

A 1aa

A 1ab

A

Example 16 Preparation of Nucleoside Thiotriphosphates

1,2,4-Triazol (42 mg, 0.6 mmol) was suspended in 1 mL of anhydrous CH₃CN. Triethylamine (0.088 ml, 0.63 mmol) was added and the mixture was vortexed to obtain a clear solution. After addition of PSCl₃ (0.01 ml, 0.1 mmol) the mixture was vortexed, followed by standing for 20 minutes, then the mixture was centrifuged. The supernatant was added to a nucleoside of Formula (A) (0.05 mmol) in trimethyl phosphate, and the mixture was kept at ambient temperature for 1 hour. Tris(tetrabutylammonium) hydrogen pyrophosphate (180 mg, 0.2 mmol) was added and the mixture was kept at room temperature for 2 hours. Under cooling with ice, the reaction was quenched with water. The resulting nucleoside 5′-triphosphate (NTP) was isolated as a mixture of diastereomers by IE chromatography on an AKTA Explorer using a HiLoad 16/10 column with Q Sepharose High Performance. Separation was done with a linear gradient of NaCl from 0 to 1N in 50 mM TRIS-buffer (pH 7.5). Fractions containing the NTP were combined, concentrated, and desalted by RP HPLC on a Synergy 4 micron Hydro-RP column (Phenominex). A linear gradient of methanol from 0 to 30% in 50 mM triethylammonium buffer was used for elution over 20 min. with a flow rate of 10 ml/min. Two separated compounds corresponding to the two Pa-diastereomers were collected.

Analytical RP HPLC was conducted using 50 mM triethylammonium acetate buffer at a pH of 7.5 and a linear gradient of acetonitrile from 0% to 25% in 7 min on a Synergy 4 micron Hydro-RP column (Phenominex). The observed retention time for each individual diastereomer is shown in Table 4 below.

TABLE 4 ³¹P ³¹P ³¹P NMR NMR NMR MS R.T. Structure Pα Pβ Pγ (M⁻) min

P(S) 42.93 −23.28 −7.94 523.1 4.40

P(R) 42.69 −22.93 −6.22 523.3 4.67 R.T. = retention time

Example 17 NS5B Inhibition Assay

The enzyme activity of NS5B570-Con1 (Delta-21) was measured as an incorporation of tritiated NMP into acid-insoluble RNA products. The complementary IRES (cIRES) RNA sequence was used as a template, corresponding to 377 nucleotides from the 3′-end of HCV (−) strand RNA of the Con-1 strain, with a base content of 21% Ade, 23% Ura, 28% Cyt, and 28% Gua. The cIRES RNA was transcribed in vitro using a T7 transcription kit (Ambion, Inc.) and purified using the Qiagen RNeasy maxi kit. HCV polymerase reactions contained 50 nM NS5B570-Con1, 50 nM cIRES RNA, about 0.5 μCi tritiated NTP, 1 μm of competing cold NTP, 20 mM NaCl, 40 mM Tris-HCl (pH 8.0), 4 mM dithiothreitol, and 4 mM MgCl₂. Standard reactions were incubated for 2 hours at 37° C., in the presence of increasing concentration of inhibitor. At the end of the reaction, RNA was precipitated with 10% TCA, and acid-insoluble RNA products were filtered on a size exclusion 96-well plate. After washing of the plate, scintillation liquid was added and radio labeled RNA products were detected according to standard procedures with a Trilux Topcount scintillation counter. The compound concentration at which the enzyme-catalyzed rate was reduced by 50% (IC₅₀) was calculated by fitting the data to a non-linear regression (sigmoidal). The IC₅₀ values were derived from the mean of several independent experiments. Compounds of Formula (I) showed activity in this assay. A value of ‘A’ indicates an IC₅₀ of <1 μM and a value of ‘B’ indicates an IC₅₀<10 μM. Compound 23a showed A activity and Compound 24a showed B activity.

Example 18 Combination of Compounds Combination Testing

Two or more test compounds were tested in combination with each other using an HCV genotype 1b HCV replicon harbored in Huh7 cells with a stable luciferase (LUC) reporter. Cells were cultured under standard conditions in Dulbecco's modified Eagle's medium (DMEM; Mediatech Inc, Herndon, Va.) containing 10% heat-inactivated fetal bovine serum (FBS; Mediatech Inc, Herndon, Va.) 2 mM L-glutamine, and nonessential amino acids (JRH Biosciences). HCV replicon cells were plated in a 96-well plate at a density of 10⁴ cells per well in DMEM with 10% FBS. On the following day, the culture medium was replaced with DMEM containing either no compound as a control, the test compounds serially diluted in the presence of 2% FBS and 0.5% DMSO, or a combination of compound 1a with one or more test compounds serially diluted in the presence of 2% FBS and 0.5% DMSO. The cells were incubated with no compound as a control, with the test compounds, or the combination of compounds for 72 hours. The direct effects of the combination of the test compounds were examined using a luciferase (LUC) based reporter as determined by the Bright-Glo Luciferase Assay (Promega, Madison, Wis.). Dose-response curves were determined for individual compounds and fixed ratio combinations of two or more test compounds.

The effects of test compound combinations were evaluated by two separate methods. In the Loewe additivity model, the experimental replicon data was analyzed by using CalcuSyn (Biosoft, Ferguson, Mo.), a computer program based on the method of Chou and Talalay. The program uses the experimental data to calculate a combination index (CI) value for each experimental combination tested. A CI value of <1 indicates a synergistic effect, a CI value of 1 indicates an additive effect, and a CI value of >1 indicates an antagonistic effect.

The second method utilized for evaluating combination effects used a program called MacSynergy II. MacSynergy II software was kindly provided by Dr. M. Prichard (University of Michigan). The Prichard Model allows for a three-dimensional examination of drug interactions and a calculation of the synergy volume (units: μM²%) generated from running the replicon assay using a checkerboard combination of two or more inhibitors. The volumes of synergy (positive volumes) or antagonism (negative volumes) represent the relative quantity of synergism or antagonism per change in the concentrations of the two drugs. Synergy and antagonism volumes are defined based on the Bliss independence model. In this model, synergy volumes of less than −25 indicate antagonistic interactions, volumes in the −25-25 range indicate additive behavior, volumes in the 25-100 range indicate synergistic behavior and volumes >100 indicate strong synergistic behavior. Determination of in vitro additive, synergistic and strongly synergistic behavior for combinations of compounds can be of utility in predicting therapeutic benefits for administering the combinations of compounds in vivo to infected patients.

The CI and synergy volume results for the combinations are provided in Table 5.

TABLE 5 Combination Synergy Volume Compound: CI at EC₅₀ (μM² %) 6002 0.69 29 3003 0.73 32 1001 0.75 104

Although the foregoing has been described in some detail by way of illustrations and examples for purposes of clarity and understanding, it will be understood by those of skill in the art that numerous and various modifications can be made without departing from the spirit of the present disclosure. Therefore, it should be clearly understood that the forms disclosed herein are illustrative only and are not intended to limit the scope of the present disclosure, but rather to also cover all modification and alternatives coming within the true scope and spirit of the invention. 

What is claimed is:
 1. A compound of Formula (I) or a pharmaceutically acceptable salt thereof:

wherein: B¹ is an optionally substituted heterocyclic base; R¹ is selected from the group consisting of O⁻, OH and an optionally substituted N-linked α-amino acid ester derivative; R² is absent or selected from the group consisting of hydrogen, an optionally substituted aryl and

wherein R⁶, R⁷ and R⁸ are independently absent or hydrogen, and n is 0 or 1; provided that when R¹ is O⁻ or OH, then R² is absent, hydrogen or

R³ is selected from the group consisting of —OR⁹ and —OC(═O)R¹⁰; R⁴ is selected from the group consisting of —OR¹¹ and —OC(═O)R¹²; R⁵ is selected from the group consisting of an optionally substituted C₂₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl and an optionally substituted C₃₋₆ cycloalkyl; R⁹ and R¹¹ are independently hydrogen or an optionally substituted C₁₋₆ alkyl; and R¹⁰ and R¹² are independently an optionally substituted C₁₋₆ alkyl or an optionally substituted C₃₋₆ cycloalkyl.
 2. The compound of claim 1, wherein R⁵ is an unsubstituted C₂₋₆ alkenyl.
 3. The compound of claim 1, wherein R⁵ is an unsubstituted C₂₋₆ alkynyl.
 4. The compound of claim 3, wherein R⁴ is —OH.
 5. The compound of claim 4, wherein R³ is —OH.
 6. The compound of claim 3, wherein R⁴ is —OC(═O)R¹², wherein R¹² is an unsubstituted C₁₋₆ alkyl.
 7. The compound of claim 6, wherein R³ is —OH.
 8. The compound of claim 3, wherein R³ is —OH.
 9. The compound of claim 3, wherein R³ is —OC(═O)R¹⁰, wherein R¹⁰ is an unsubstituted C₁₋₆ alkyl.
 10. The compound of claim 9, wherein R⁴ is —OH.
 11. The compound of claim 3, wherein R¹ is O⁻ or OH; and R² is absent or hydrogen.
 12. The compound of claim 3, wherein leis an optionally substituted N-linked α-amino acid ester derivative; and R² is an optionally substituted aryl.
 13. The compound of claim 3, wherein R² is

n is 0 R¹ is O⁻ or OH; and R⁷ and R⁸ are independently absent or hydrogen.
 14. The compound of claim 3, wherein R² is

n is 1; R¹ is O⁻ or OH; and R⁶, R⁷ and R⁸ are independently absent or hydrogen.
 15. The compound of claim 3, wherein B¹ is selected from the group consisting of:


16. The compound of claim 15, wherein B¹ is


17. A pharmaceutical composition comprising a therapeutically effective amount of a compound of claim 1, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier, diluent, excipient or combination thereof.
 18. A method for ameliorating or treating an HCV infection comprising administering to a subject suffering from an HCV infection a therapeutically effective amount of a compound of claim 1, or a pharmaceutically acceptable salt thereof.
 19. A method of ameliorating or treating a HCV infection comprising contacting a cell infected with the HCV virus with a therapeutically effective amount of a compound of claim 1, in combination with a second anti-HCV agent selected from the group consisting of a HCV protease inhibitor, a HCV polymerase inhibitor and a NS5A inhibitor.
 20. The method of claim 19, wherein the second anti-HCV agent is selected from the group consisting of

or a pharmaceutically acceptable salt of any of the aforementioned compounds. 